File Coverage

blib/lib/MRS/Client.pm
Criterion Covered Total %
statement 13 15 86.6
branch n/a
condition n/a
subroutine 5 5 100.0
pod n/a
total 18 20 90.0


line stmt bran cond sub pod time code
1             #-----------------------------------------------------------------
2             # MRS::Client
3             # Authors: Martin Senger
4             # For copyright and disclaimer see MRS::Client pod.
5             #
6             # ABSTRACT: A SOAP-based client of the MRS Retrieval server
7             # PODNAME: MRS::Client
8             #-----------------------------------------------------------------
9 4     4   99561 use strict;
  4         12  
  4         170  
10 4     4   22 use warnings;
  4         7  
  4         239  
11              
12             package MRS::Client;
13              
14             our $VERSION = '1.0.1'; # VERSION
15              
16 4     4   22 use vars qw( $AUTOLOAD );
  4         7  
  4         217  
17 4     4   30 use Carp;
  4         7  
  4         319  
18 4     4   3252 use XML::Compile::SOAP11 2.26;
  0            
  0            
19             use XML::Compile::WSDL11;
20             use XML::Compile::Transport::SOAPHTTP;
21             use File::Basename;
22             use Data::Dumper;
23              
24             use MRS::Constants;
25             use MRS::Client::Databank;
26             use MRS::Client::Find;
27             use MRS::Client::Blast;
28             use MRS::Client::Clustal;
29              
30             #-----------------------------------------------------------------
31             #
32             # Expoted constants
33             #
34             #-----------------------------------------------------------------
35             use constant DEFAULT_SEARCH_ENDPOINT => 'http://mrs.cmbi.ru.nl/m6/mrsws/search';
36             use constant DEFAULT_BLAST_ENDPOINT => 'http://mrs.cmbi.ru.nl/m6/mrsws/blast';
37             use constant DEFAULT_CLUSTAL_ENDPOINT => 'http://mrs.cmbi.ru.nl/m6/mrsws/clustal';
38             use constant DEFAULT_ADMIN_ENDPOINT => 'http://mrs.cmbi.ru.nl/m6/mrsws/admin';
39             use constant DEFAULT_SEARCH_WSDL => 'search.wsdl.template';
40             use constant DEFAULT_BLAST_WSDL => 'blast.wsdl.template';
41             use constant DEFAULT_CLUSTAL_WSDL => 'clustal.wsdl.template';
42             use constant DEFAULT_ADMIN_WSDL => 'admin.wsdl.template';
43             use constant DEFAULT_SEARCH_WSDL_6 => 'search.wsdl.template.v6';
44             use constant DEFAULT_BLAST_WSDL_6 => 'blast.wsdl.template.v6';
45             use constant DEFAULT_CLUSTAL_WSDL_6 => 'clustal.wsdl.template'; # no ClustalW in MRS 6
46             use constant DEFAULT_ADMIN_WSDL_6 => 'admin.wsdl.template'; # no Admin in MRS 6
47             use constant DEFAULT_SEARCH_SERVICE => 'mrsws_search';
48             use constant DEFAULT_BLAST_SERVICE => 'mrsws_blast';
49             use constant DEFAULT_CLUSTAL_SERVICE => 'mrsws_clustal';
50             use constant DEFAULT_ADMIN_SERVICE => 'mrsws_admin';
51              
52              
53             #-----------------------------------------------------------------
54             # A list of allowed options/arguments (used in the new() method)
55             #-----------------------------------------------------------------
56             {
57             my %_allowed =
58             (
59             search_url => 1,
60             blast_url => 1,
61             clustal_url => 1,
62             admin_url => 1,
63              
64             search_service => 1,
65             blast_service => 1,
66             clustal_service => 1,
67             admin_service => 1,
68              
69             search_wsdl => 1,
70             blast_wsdl => 1,
71             clustal_wsdl => 1,
72             admin_wsdl => 1,
73              
74             host => 1,
75             mrs_version => 1,
76             debug => 1,
77             );
78              
79             sub _accessible {
80             my ($self, $attr) = @_;
81             exists $_allowed{$attr};
82             }
83             }
84              
85             #-----------------------------------------------------------------
86             # Deal with 'set' and 'get' methods.
87             #-----------------------------------------------------------------
88             sub AUTOLOAD {
89             my ($self, $value) = @_;
90             my $ref_sub;
91             if ($AUTOLOAD =~ /.*::(\w+)/ && $self->_accessible ("$1")) {
92              
93             # get/set method
94             my $attr_name = "$1";
95             $ref_sub =
96             sub {
97             # get method
98             local *__ANON__ = "__ANON__$attr_name" . "_" . ref ($self);
99             my ($this, $value) = @_;
100             return $this->{$attr_name} unless defined $value;
101              
102             # set method
103             $this->{$attr_name} = $value;
104             return $this->{$attr_name};
105             };
106              
107             } else {
108             throw ("No such method: $AUTOLOAD");
109             }
110              
111             ## no critic
112             no strict 'refs';
113             *{$AUTOLOAD} = $ref_sub;
114             use strict 'refs';
115             return $ref_sub->($self, $value);
116             }
117              
118             #-----------------------------------------------------------------
119             # Keep it here! The reason is the existence of AUTOLOAD...
120             #-----------------------------------------------------------------
121             sub DESTROY {
122             }
123              
124             #-----------------------------------------------------------------
125             # new
126             #-----------------------------------------------------------------
127             sub new {
128             my ($class, @args) = @_;
129              
130             # create an object
131             my $self = bless {}, ref ($class) || $class;
132              
133             # set default values
134             $self->search_url ($ENV{'MRS_SEARCH_URL'} or DEFAULT_SEARCH_ENDPOINT);
135             $self->blast_url ($ENV{'MRS_BLAST_URL'} or DEFAULT_BLAST_ENDPOINT);
136             $self->clustal_url ($ENV{'MRS_CLUSTAL_URL'} or DEFAULT_CLUSTAL_ENDPOINT);
137             $self->admin_url ($ENV{'MRS_ADMIN_URL'} or DEFAULT_ADMIN_ENDPOINT);
138             $self->search_service (DEFAULT_SEARCH_SERVICE);
139             $self->blast_service (DEFAULT_BLAST_SERVICE);
140             $self->clustal_service (DEFAULT_CLUSTAL_SERVICE);
141             $self->admin_service (DEFAULT_ADMIN_SERVICE);
142              
143             $self->{compiled_operations} = {};
144              
145             # set all @args into this object with 'set' values
146             my (%args) = (@args == 1 ? (value => $args[0]) : @args);
147             foreach my $key (keys %args) {
148             ## no critic
149             no strict 'refs';
150             $self->$key ($args {$key});
151             }
152             $self->host ($ENV{'MRS_HOST'}) if $ENV{'MRS_HOST'};
153              
154             # set MRS version
155             $self->{mrs_version} = $ENV{'MRS_VERSION'} if $ENV{'MRS_VERSION'};
156             $self->{mrs_version} = 6 unless $self->{mrs_version};
157              
158             # done
159             return $self;
160             }
161              
162             #-----------------------------------------------------------------
163             #
164             #-----------------------------------------------------------------
165             sub is_v6 {
166             my $self = shift;
167             return (defined $self->{mrs_version} and $self->{mrs_version} eq '6');
168             }
169              
170             #-----------------------------------------------------------------
171             #
172             #-----------------------------------------------------------------
173             sub host {
174             my ($self, $host) = @_;
175             return $self->{host} unless $host;
176              
177             my $current = $self->{host};
178              
179             # use $host and default ports,
180             # unless some URLs were given specifically
181             if ( $self->search_url eq DEFAULT_SEARCH_ENDPOINT or
182             ($current and $self->search_url eq "http://$current:18081/") ) {
183             $self->search_url ("http://$host:18081/");
184             }
185             if ( $self->blast_url eq DEFAULT_BLAST_ENDPOINT or
186             ($current and $self->blast_url eq "http://$current:18082/") ) {
187             $self->blast_url ("http://$host:18082/");
188             }
189             if ( $self->clustal_url eq DEFAULT_CLUSTAL_ENDPOINT or
190             ($current and $self->clustal_url eq "http://$current:18083/") ) {
191             $self->clustal_url ("http://$host:18083/");
192             }
193             if ( $self->admin_url eq DEFAULT_ADMIN_ENDPOINT or
194             ($current and $self->admin_url eq "http://$current:18084/") ) {
195             $self->admin_url ("http://$host:18084/");
196             }
197              
198             $self->{host} = $host;
199             }
200              
201             #-----------------------------------------------------------------
202             # Read the WSDL file, create from it a proxy and store it in
203             # itself. Do it only once unless $force_creation is defined.
204             #
205             # $ptype tells what kind of proxy to create: search, blast, clustal or
206             # admin.
207             #
208             # What WSDL file is read: It reads file previously set by one of the
209             # methods (depending which proxy should be read): search_wsdl(),
210             # blast_wsdl(), clustal_wsdl or admin_wsdl(). If such method was not
211             # called, the default WSDL is read from the file named '$ptype
212             # . _proxy', located in the same directory as this module.
213             # -----------------------------------------------------------------
214             sub _create_proxy {
215             my ($self, $ptype, $default_wsdl, $force_creation) = @_;
216             $self->{$ptype . '_proxy'} = undef if $force_creation;
217             if (not defined $self->{$ptype . '_proxy'}) {
218             my $wsdl;
219             if (not defined $self->{$ptype . '_wsdl'}) {
220             $wsdl = _readfile ( (fileparse (__FILE__))[-2] . $self->_default_wsdl ($ptype) );
221             $wsdl =~ s/\${LOCATION}/$self->{$ptype . '_url'}/eg;
222             $wsdl =~ s/\${SERVICE}/$self->{$ptype . '_service'}/eg;
223             } else {
224             $wsdl = XML::LibXML->new->parse_file ($self->{$ptype . '_wsdl'});
225             }
226             $self->{$ptype . '_proxy'} = XML::Compile::WSDL11->new ($wsdl);
227             }
228             }
229              
230             sub _default_wsdl {
231             my ($self, $ptype) = @_;
232              
233             if ($self->is_v6) {
234             return DEFAULT_SEARCH_WSDL_6 if $ptype eq 'search';
235             return DEFAULT_BLAST_WSDL_6 if $ptype eq 'blast';
236             return DEFAULT_CLUSTAL_WSDL_6 if $ptype eq 'clustal';
237             return DEFAULT_ADMIN_WSDL_6 if $ptype eq 'admin';
238             } else {
239             return DEFAULT_SEARCH_WSDL if $ptype eq 'search';
240             return DEFAULT_BLAST_WSDL if $ptype eq 'blast';
241             return DEFAULT_CLUSTAL_WSDL if $ptype eq 'clustal';
242             return DEFAULT_ADMIN_WSDL if $ptype eq 'admin';
243             }
244             die "Uknown proxy type '" . $ptype . "'\n";
245             }
246              
247             sub _readfile {
248             my $filename = shift;
249             my $data;
250             {
251             local $/=undef;
252             open my $file, '<', $filename or croak "Couldn't open file $filename: $!\n";
253             $data = <$file>;
254             close $file;
255             }
256             return $data;
257             }
258              
259             #-----------------------------------------------------------------
260             # Make a SOAP call to a MRS server, using $proxy (created usually by
261             # _create_proxy), invoking $operation with $parameters (a hash
262             # reference).
263             # -----------------------------------------------------------------
264             sub _call {
265             my ($self, $proxy, $operation, $parameters) = @_;
266              
267             # the compiled client for the same operation may be already
268             # cached; if not then compile it and save for later
269             my $call = $self->{compiled_operations}->{$operation};
270             unless (defined $call) {
271             $call = $proxy->compileClient ($operation);
272             $self->{compiled_operations}->{$operation} = $call;
273             }
274              
275             # make a SOAP call
276             my ($answer, $trace) = $call->( %$parameters );
277              
278             if ($self->{debug}) {
279             print "OPERATION: $operation, PARAMS:\n".Dumper ($parameters);
280             print "RESPONSE:\n".Dumper ($answer);
281             print $trace->printResponse unless defined $answer;
282             }
283             # print "CALL TRA:\n".Dumper ($trace);
284             # $trace->printTimings;
285             # $trace->printRequest;
286             # $trace->printResponse;
287              
288             croak 'ERROR: ' . $answer->{Fault}->{'faultstring'} . "\n"
289             if defined $answer and defined $answer->{Fault};
290              
291             return $answer;
292             }
293              
294             #-----------------------------------------------------------------
295             # Factory method for creating one or more databanks:
296             # it returns an array of MRS::Client::Databank if $db is undef or empty or 'all'
297             # else it returns a databank indicated by $db (which is an Id)
298             #-----------------------------------------------------------------
299             sub db {
300             my ($self, $db) = @_;
301              
302             return MRS::Client::Databank->new (id => $db, client => $self)
303             if $db and $db ne 'all';
304              
305             $self->_create_proxy ('search');
306             my $answer = $self->_call (
307             $self->{search_proxy}, 'GetDatabankInfo', { db => 'all' });
308             my @dbs = ();
309             return @dbs unless defined $answer;
310             foreach my $info (@{ $answer->{parameters}->{info} }) {
311             push (@dbs, MRS::Client::Databank->new (%$info, client => $self, info_retrieved => 1));
312             }
313             return @dbs;
314             }
315              
316             #-----------------------------------------------------------------
317             # The same as db->find but acting on all available databanks
318             #-----------------------------------------------------------------
319             sub find {
320             my $self = shift;
321              
322             my $multi = MRS::Client::MultiFind->new ($self, @_);
323             # $multi->{client} = $self;
324              
325             # create individual finds for each available databank
326             $multi->{args} = \@_; # will be needed for cloning
327             $multi->{children} = $multi->_read_first_hits;
328             $multi->{current} = 0;
329              
330             # do we have any hits, at all?
331             $multi->{eod} = 1 if @{ $multi->{children} } == 0;
332              
333             return $multi;
334             }
335              
336             #-----------------------------------------------------------------
337             # Create a blast object - it can be used for running more jobs, with
338             # different parameters [TBD: , giving a statistics about all jobs?]
339             #
340             # Create maximum one blast object; we do not need more.
341             # -----------------------------------------------------------------
342             sub blast {
343             my $self = shift;
344             return $self->{blastobj} if $self->{blastobj};
345             $self->{blastobj} = MRS::Client::Blast->_new (client => $self);
346             return $self->{blastobj};
347             }
348              
349             #-----------------------------------------------------------------
350             # Create a clustal object; a simple factory method.
351             # -----------------------------------------------------------------
352             sub clustal {
353             my $self = shift;
354             croak "ClustalW service is not available in MRS server version 6 and above.\n"
355             if $self->is_v6;
356             return MRS::Client::Clustal->_new (client => $self);
357             }
358              
359             #-----------------------------------------------------------------
360             #
361             # Admin calls ... work in progress, and not really supported, AND it
362             # disappeared completely in MRS 6
363             #
364             #-----------------------------------------------------------------
365              
366             #-----------------------------------------------------------------
367             # Return a script that parses a databank. $script is its name.
368             #-----------------------------------------------------------------
369             sub parser {
370             my ($self, $script) = @_;
371              
372             croak "Empty parser name. Cannot retrieve it, I am afraid.\n"
373             unless $script;
374              
375             $self->_create_proxy ('admin');
376             my $answer = $self->_call (
377             $self->{admin_proxy}, 'GetParserScript',
378             { script => $script,
379             format => 'plain' });
380             return $answer->{parameters}->{response};
381             }
382              
383             1;
384              
385              
386             =pod
387              
388             =head1 NAME
389              
390             MRS::Client - A SOAP-based client of the MRS Retrieval server
391              
392             =head1 VERSION
393              
394             version 1.0.1
395              
396             =head1 SYNOPSIS
397              
398             # 1. create a client that does all the work:
399             use MRS::Client;
400              
401             # ...by default it connects to the MRS service at http://mrs.cmbi.ru.nl/m6
402             my $client = MRS::Client->new();
403              
404             # ...or let the client talk to your own MRS servers
405             my $client = MRS::Client->new ( search_url => 'http://localhost:18081/',
406             blast_url => 'http://localhost:18082/',;
407             clustal_url => 'http://localhost:18083/'); # this only for MRS 5
408              
409             # ...or specify only a host, assuming the default ports are used
410             my $client = MRS::Client->new ( host => 'localhost');
411              
412             # 2a. make various queries to a selected database:
413             print $client->db ('uniprot')->find ('sapiens')->count;
414             175642
415              
416             print $client->db ('uniprot')->find ('sapiens')->next;
417             ID Q14547_HUMAN Unreviewed; 60 AA.
418             AC Q14547;
419             DT 01-NOV-1996, integrated into UniProtKB/TrEMBL.
420             DT 01-NOV-1996, sequence version 1.
421             DT 19-JAN-2010, entry version 51.
422             DE SubName: Full=Homeobox-like;
423             DE Flags: Fragment;
424             OS Homo sapiens (Human).
425             ...
426              
427             # show id, relevance score and title of two terms connected by AND
428             my $query = $client->db ('enzyme')->find ('and' => ['snake', 'human'],
429             'format' => MRS::EntryFormat->HEADER);
430             while (my $record = $query->next) {
431             print $record . "\n";
432             }
433             enzyme 3.4.21.95 17.6527424 Snake venom factor V activator.
434              
435             # ...show only title, but now the same two terms are connected by OR
436             my $query = $client->db ('enzyme')->find ('or' => ['snake', 'human'],
437             'format' => MRS::EntryFormat->TITLE);
438             while (my $record = $query->next) {
439             print $record . "\n";
440             }
441             Snake venom factor V activator.
442             Jararhagin.
443             Bothropasin.
444             Trimerelysin I.
445             ...
446              
447             # combine term-based (ranked) query with additional boolean expression
448             my $query = $client->db ('uniprot')->find ('and' => ['snake', 'human'],
449             query => 'NOT (kinase OR reductase)',
450             'format' => MRS::EntryFormat->HEADER);
451             print "Count: " . $query->count . "\n";
452             while (my $record = $query->next) {
453             print $record . "\n";
454             }
455             Count: 75
456             nxs11_micsu 23.3861961 Short neurotoxin MS11;
457             nxl2_micsu 22.7922745 Long neurotoxin MS2;
458             nxl5_micsu 22.2648716 Long neurotoxin MS5;
459             ...
460              
461             # 2b. explore full information about a database
462             print $client->db ('enzyme');
463              
464             # ...or extract only information parts you want
465             print $client->db ('enzyme')->version;
466             print $client->db ('enzyme')->count;
467              
468             # 3. Or, almost all functionality is also available in a provided
469             # script I:
470              
471             mrsclient -h
472             mrsclient -C
473             mrsclient -c -n insulin
474             mrsclient -c -p -d enzyme -a 'endothelin tyrosine'
475              
476             # 4. Run blastp on protein sequences:
477              
478             my @run_args = (fasta_file => 'protein.fasta', db => 'uniprot');
479             my $job = $client->blast->run (@run_args);
480             print STDERR 'JOB ID: ' . $job->id . ' [' . $job->status . "]\n";
481             print $job;
482             while (not $job->completed) {
483             print STDERR 'Waiting for 10 seconds... [status: ' . $job->status . "]\n";
484             sleep 10;
485             }
486             print $job->error if $job->failed;
487             print $job->results;
488              
489             # Or, use for it the provide script I:
490              
491             mrsblast -h
492             mrsblast -i /tmp/snake.protein.fasta -d uniprot -x result.xml
493              
494             # 5. Run clustalw multiple alignment:
495             # (available only for MRS version 5 and lower)
496              
497             my $result = $client->clustal->run (fasta_file => 'multiple.fasta' );
498             print "ERROR: " . $result->failed if $result->failed;
499             print $result->diagnostics;
500             print $result;
501              
502             # Or, use for it the provide script I:
503              
504             mrsclustal -h
505             mrsclustal -i multiple.fasta
506              
507             =head1 DESCRIPTION
508              
509             This module is a SOAP-based (Web Services) client that can talk, and
510             get data from an B, a search engine for biological and
511             medical databanks that searches well over a terabyte of indexed
512             text. See details about MRS and its author Maarten Hekkelman in
513             L.
514              
515             Because this module is only a client, you need an MRS server
516             running. You can install your own (see details in the MRS
517             distribution), or you need to know a site that runs it. By default,
518             this module contacts the MRS server at CMBI
519             (F).
520              
521             The usual scenario is the following:
522              
523             =over
524              
525             =item *
526              
527             Create a new instance of a client by calling:
528              
529             my $client = MRS::Client->new (%args);
530              
531             =item *
532              
533             Optionally, find out what databanks are available by calling:
534              
535             my @ids = map { $_->id } $client->db;
536             print "Names:\n" . join ("\n", @ids) . "\n";
537              
538             =item *
539              
540             Make one or more queries on a selected databanks and iterate over the
541             result:
542              
543             my $query = $client->db ('enzyme')->find (['cone', 'snail']);
544             while (my $record = $query->next) {
545             print $record . "\n";
546             }
547              
548             Or, make the same query on all available databanks:
549              
550             my $query = $client->find (['cone', 'snail']);
551             while (my $record = $query->next) {
552             print $record . "\n";
553             }
554              
555             The format of returned records is specified by a parameter of the
556             I method (see more in L<"METHODS">).
557              
558             =item *
559              
560             Additionally, this module provides access to I program, using
561             MRS indexed databases. And it can invoke multiple alignment program
562             I.
563              
564             =back
565              
566             =head1 ATTENTION
567              
568             I C: Because
569             the latest version of MRS server (version 6) is not backward
570             compatible with the previous version of the MRS server (version 5),
571             there are some significant (but fortunately not huge) changes needed
572             in your programs. Read details in L.
573              
574             =head1 METHODS
575              
576             =head2 MRS::Client
577              
578             The main module is C. It lets the user specify which MRS
579             server to use, and few other global options. It also has a factory
580             method for creating individual databanks objects. Additionally, it
581             allows making query over all databanks. Finally, it covers all the
582             SOAP communication with the server.
583              
584             =head3 new
585              
586             use MRS::Client;
587             my $client = MRS::Client->new (@parameters);
588              
589             The parameters are name-value pairs. The following names are recognized:
590              
591             =over
592              
593             =item search_url, blast_url, clustal_url
594              
595             The URLs of the individual MRS servers, one providing searches (the
596             main one), one running blast and one running clustal. Default values
597             lead your searches to CMBI. If you have installed MRS servers on your
598             own site, and you are using the default values coming with the MRS
599             distribution, you create a client by (but see below parameter I
600             for a shortcut):
601              
602             my $client = MRS::Client->new ( search_url => 'http://localhost:18081/',
603             blast_url => 'http://localhost:18082/',
604             clustal_url => 'http://localhost:18083/', # this only for MRS 5
605             );
606              
607             Technical detail: These URLs will be used in the location field of the
608             WSDL description.
609              
610             Alternatively, you can specify these parameters by environment
611             variables (because they will be probably same for most users from the
612             same site). The parameters, however, still have precedence over the
613             values of environment variables (even if they exist). The variables
614             are: I, I and I.
615              
616             B Some sites may not have all MRS servers running.
617              
618             =item host
619              
620             A shortcut for specifying a host name in all URLs. The same as in the
621             above example can be accomplished by:
622              
623             my $client = MRS::Client->new (host => 'localhost');
624              
625             Again, you can specify this parameter by an environment variables
626             MRS_HOST.
627              
628             =item search_service, blast_service, clustal_service
629              
630             The MRS servers are SOAP-based Web Services. Every Web Service has its
631             own I (the name used in the WSDL). You can change this
632             service name if you are accessing site where they use non-default
633             names. The default names - I guess almost always used - are:
634             mrsws_search, mrsws_blast, mrsws_clustal.
635              
636             =item search_wsdl, blast_wsdl, clustal_wsdl
637              
638             You can also specify your own WSDL file, each one for each set of
639             operations. It is meant more for debugging purposes because this
640             C module understands only current operations and adding
641             new ones to a new WSDL does not magically start using them. These
642             parameters may be useful when extending the C.
643              
644             =back
645              
646             =head3 setters/getters
647              
648             The same names as the argument names described above can be used as
649             method names to get or set the parameter value. A method without an
650             argument gets the current value, a method with an argument sets the
651             new value. For example:
652              
653             print $client->search_url;
654             $client->search_url ('http://my.own.server/mrs/search');
655              
656             =head3 db
657              
658             This is a factory method creating one or more databanks instances. It
659             accepts a single argument, a databank ID:
660              
661             print $client->db ('enzyme');
662              
663             Id: enzyme
664             Name: Enzyme
665             Version: 2013-05-27
666             Count: 6115
667             URL: http://ca.expasy.org/enzyme/
668             Parser: enzyme
669             Files:
670             Version: 2013-05-27
671             Modified: 2013-05-27 11:46 GMT
672             Entries count: 6115
673             Raw data size: 7436504
674             File size: 45563041
675             Unique Id: fc0540bd-58a2-4de7-b3ff-6daff64ca13c
676             Indices:
677             enzyme text 14881 Unique
678             enzyme de 3650 Unique Description
679             enzyme dr 420832 Unique Database Reference
680             enzyme id 6114 Unique Identification
681             enzyme pr 398 Unique Prosite Reference
682              
683             You can find out what databanks IDs are available by:
684              
685             print join ("\n", map { $_->id } $client->db);
686              
687             Which brings us to the usage of the I method without any
688             parameter, or with an empty parameter. In such cases, it creates an
689             array of C instances.
690              
691             =head3 find
692              
693             Make the same query to all databanks. The parameters are the same as
694             for the I method called for an individual databank (see below).
695              
696             print "Databank\tID\tScore\tTitle\n";
697             my $query = $client->find ('and' => ['cone', 'snail'],
698             'format' => MRS::EntryFormat->HEADER);
699             while (my
700             $record = $query->next) {
701             print $record . "\n";
702             }
703             print $query->count . "\n";
704              
705             Databank ID Score Title
706             interpro ipr020242 29.7122746 Conotoxin I2-superfamily
707             interpro ipr012322 27.8191032 Conotoxin, delta-type, conserved site
708             ...
709             omim 114020 3.40963793 cadherin 2
710             omim 192090 3.40769672 cadherin 1
711             sprot cxd6d_concn 19.4017849 Delta-conotoxin CnVID;
712             sprot cxd6c_concn 19.3984871 Delta-conotoxin CnVIC;
713             ...
714             taxonomy 6495 53.980381 Conus tulipa fish-hunting cone snail
715             trembl q71ks8_contu 22.1446457 Four-loop conotoxin preproprotein;
716             trembl q9u7q6_contu 20.6787205 Calmodulin;
717             ...
718             149
719              
720             The query (method I) returns entries sequentially, one databank
721             after another. As with individual databanks, even here you can select
722             maximum number of entries to deliver - the number is applied for each
723             databank separately:
724              
725             my $query = $client->find ('and' => ['cone', 'snail'],
726             max_entries => 2,
727             'format' => MRS::EntryFormat->HEADER);
728             while (my
729             $record = $query->next) {
730             print $record . "\n";
731             }
732              
733             interpro ipr020242 29.7122746 Conotoxin I2-superfamily
734             interpro ipr012322 27.8191032 Conotoxin, delta-type, conserved site
735             omim 114020 3.40963793 cadherin 2
736             omim 192090 3.40769672 cadherin 1
737             sprot cxd6d_concn 19.4017849 Delta-conotoxin CnVID;
738             sprot cxd6c_concn 19.3984871 Delta-conotoxin CnVIC;
739             taxonomy 6495 53.980381 Conus tulipa fish-hunting cone snail
740             trembl q71ks8_contu 22.1446457 Four-loop conotoxin preproprotein;
741             trembl q9u7q6_contu 20.6787205 Calmodulin;
742              
743             =head3 blast
744              
745             $client->blast
746              
747             A factory method for creating a singleton instance of
748             F.
749              
750             =head3 clustal
751              
752             $client->clustal
753              
754             A factory method for creating instances of F.
755              
756             =head2 MRS::Client::Databank
757              
758             This package represents an MRS databank and allows to query it. Each
759             databank consists of one or more files (represented by
760             C) and of indices
761             (C).
762              
763             A databank instance can be created by a I method but usually it
764             is created by a factory method available in the C:
765              
766             my $db = $client->db ('enzyme');
767              
768             The factory method, as well as the I method, creates only a
769             "shell" databank instance - that is good enough for making queries but
770             which does not contain any databank properties (name, indices,
771             etc.) yet. The properties will be fetched from the MRS server only when
772             you ask for them (using the "getter" methods described below).
773              
774             =head3 new
775              
776             The only, and mandatory, parameter is I:
777              
778             $db = MRS::Client::Databank->new (id => 'interpro');
779              
780             The arguments syntax (the hash) is prepared for more arguments later
781             (perhaps). But it should not bother you because you would rarely use
782             this method - having the factory method I in the client.
783              
784             I Do not use this method directly, or check first how
785             it is used in the module C.
786              
787             =head3 find
788              
789             This is the crucial method of the whole C module. It
790             queries a databank and returns an C instance that
791             can be used to iterate over found entries.
792              
793             It takes many arguments. At least one of the "query" arguments (which
794             are I, I and I) must be supplied; other arguments are
795             optional.
796              
797             The arguments can always be specified as a hash, but for usual cases
798             there are few shortcuts. Let's look at the arguments as used in the
799             hash:
800              
801             =over
802              
803             =item C
804              
805             The value is an array reference where elements are terms that will be
806             combined by the AND boolean operator in a ranked query. For example:
807              
808             $find = $db->find ('and' => ['human', 'snake']);
809              
810             This argument can also be used directly, not as a hash, assuming that
811             you do not need to use any other arguments:
812              
813             $find = $db->find (['human', 'snake']);
814              
815             =item C
816              
817             The value is an array reference where elements are terms that will be
818             combined by the OR boolean operator in a ranked query. For example:
819              
820             $find = $db->find ('or' => ['human', 'snake']);
821              
822             There can be either an I or an I argument, but not both. If
823             there are used both, a warning is issued and the I one will take
824             precedence.
825              
826             =item C
827              
828             The value is an expression, usually using some boolean operators (in
829             upper cases!):
830              
831             $find = $db->find (query => 'hemoglobinase AND NOT human');
832              
833             If there are no boolean operators, it is used as a single term. For
834             example, these are equivalent:
835              
836             $find = $db->find (query => 'hemoglobinase activity');
837             $find = $db->find ('and' => ['hemoglobinase activity']);
838              
839             You can also use both, I or I, and I. The query then
840             is an additional filter applied to the results found by the I or
841             I terms. For example:
842              
843             $find = $db->find ('and' => ['human', 'snake'],
844             query => 'NOT neurotoxin');
845              
846             As a shortcut, the query parameter can also be used without a hash,
847             assuming again that you do not need to use any other arguments:
848              
849             $find = $db->find ('hemoglobinase AND NOT human');
850              
851             =item C
852              
853             B This argument is used only by MRS version 5,
854             See L for details.
855              
856             The ranked queries (the ones achieved by I or I arguments)
857             have assigned relevance score to their hits. The relevance score
858             depends on the used algorithm. The available values for this arguments
859             are defined in C:
860              
861             package MRS::Algorithm;
862             use constant {
863             VECTOR => 'Vector',
864             DICE => 'Dice',
865             JACCARD => 'Jaccard',
866             };
867              
868             The default algorithm is "Vector". For example (using the format
869             "header" - which is the only one that shows relevance scores):
870              
871             $client->$db('enzyme')->find ('and' => 'venom',
872             algorithm => MRS::Algorithm->Dice,
873             max_entries => 3,
874             'format' => MRS::EntryFormat->HEADER);
875             enzyme 3.4.24.43 14.9607477 Atroxase.
876             enzyme 3.4.24.49 13.6817474 Bothropasin.
877             enzyme 3.4.24.73 13.2007284 Jararhagin.
878              
879             $client->$db('enzyme')->find ('and' => 'venom',
880             algorithm => MRS::Algorithm->Vector,
881             max_entries => 3,
882             'format' => MRS::EntryFormat->HEADER);
883             enzyme 3.1.15.1 21.6520195 Venom exonuclease.
884             enzyme 3.4.21.60 19.3931656 Scutelarin.
885             enzyme 5.1.1.16 16.7410889 Protein-serine epimerase.
886              
887             =item C, C, C
888              
889             These arguments do not affect the query itself but it tells which
890             entries from the found ones to retrieve (by the I method - see
891             below).
892              
893             All these three arguments have an integer value.
894              
895             C tells to skip entries at the beginning of the whole result
896             and start returning only with the entry with this order number. The
897             counting start from 1.
898              
899             C is the same as the C, except the counting starts from
900             zero.
901              
902             C is the maximum entries to retrieve.
903              
904             =item C
905              
906             This argument also does not affect the query itself but it defines the
907             format of the returned entries. The available values for this arguments
908             are defined in C:
909              
910             package MRS::EntryFormat;
911             use constant {
912             PLAIN => 'plain',
913             TITLE => 'title',
914             HTML => 'html',
915             FASTA => 'fasta',
916             SEQUENCE => 'sequence',
917             HEADER => 'header',
918             };
919              
920             The default format is 'plain'. The 'fasta' and 'sequence' formats are
921             available only for databanks that have sequence data. For all formats,
922             except for the 'header', the entries are returned as strings. For
923             'header', the entries are instances of C.
924              
925             Be aware that C is also a built-in Perl function, so better
926             quote it when used as a hash key (it seems to work also without quotes
927             except the emacs TAB key is confused if there are no surrounding
928             quotes; just a minor annoyance).
929              
930             =item C
931              
932             This argument (C) enhances the C argument. It
933             is used (at least at the moment) only for HTML format; for other
934             formats, it is ignored. See, however, the L about the
935             abandoned HTML format.
936              
937             Be aware, however, that the C depends on the structure of the
938             HTML provided by the MRS. This structure is not defined in the MRS
939             server API, so it can change easily. It even depends on the way how
940             the authors write their parsing scripts. When the HTML
941             output changes this module must be changed, as well. Caveat emptor.
942              
943             The C is a hashref with keys that change (slightly or
944             significantly) the returned HTML. Here are all possible keys
945             (with a randomly picked up values):
946              
947             xformat => { MRS::XFormat::CSS_CLASS() => 'mrslink',
948             MRS::XFormat::URL_PREFIX() => 'http://cbrcgit:8080/mrs-web/'
949             MRS::XFormat::REMOVE_DEAD() => 1, # 'or' => ['...']
950             MRS::XFormat::ONLY_LINKS() => 1 }
951              
952             C specifies a CSS-class name that will be
953             added to all C tags in the returned HTML. It allows, for example,
954             an easy post-processing by various JavaScript libraries. For example,
955             if the original HTML contains:
956              
957            
958              
959             it will become (using the value shown above):
960              
961            
962              
963             C helps to keep the returned HTML
964             independent on the machine where it was created. This option pre-pends
965             the given prefix to the relative URLs in the hyperlinks that point to
966             the data in an MRS web application. For example, if the original HTML
967             contains:
968              
969            
970              
971             it will become:
972              
973            
974              
975             Other hyperlinks - those not starting with C or C - are
976             not affected.
977              
978             C deals with the fact that the MRS server
979             creates hyperlinks pointing to other MRS databanks without checking
980             that they actually exists in the local MRS installation. This may be
981             fixed later (quoting Maarten) but before it happens this option (if with a true
982             value) removes (from the returned HTML) all hyperlinks that point to
983             the not-installed MRS databanks. For example, if the original HTML has
984             these hyperlinks:
985              
986             AF536179
987             D00735
988             1VZN
989             2FK4
990              
991             and the C database is not locally installed, the returned HTML
992             will change to:
993              
994             AF536179
995             D00735
996             1VZN
997             2FK4
998              
999             There is a small caveat, however. The MRS::Client needs to know what
1000             databanks are installed. It finds out by asking the MRS server by
1001             using the method C (explained elsewhere in this document). This
1002             method returns much more than is needed, so it can be slightly
1003             expensive. Therefore, if your concern is the highest speed, you can
1004             help the MRS::Client by providing a list of databanks that you know
1005             you have installed. Actually, in most cases, you can create such list
1006             also by calling the C method but depending on your code you can
1007             call it just ones an reuse it. For example, if you wish to keep
1008             hyperlinks only for 'uniprot' and 'embl', you specify;
1009              
1010             xformat => { MRS::XFormat::REMOVE_DEAD() => ['uniprot', 'embl'] }
1011              
1012             Finally, there is an option C. It has a very
1013             specific function: to extract and return C the hyperlinks, not
1014             the whole HTML. It is, therefore, predestined for further
1015             post-processing. Note that all changes in the hyperlinks described
1016             earlier are also applied here (e.g. adding an absolute URL or a CSS
1017             class).
1018              
1019             When this option is used, the whole method "$find->next" (or
1020             "db->entry") returns a reference to an array of extracted
1021             hyperlinks:
1022              
1023             my $find = $client->db('sprot')->find
1024             (and => ['DNP_DENAN'],
1025             'format' => MRS::EntryFormat->HTML,
1026             xformat => {
1027             MRS::XFormat::ONLY_LINKS() => 1,
1028             MRS::XFormat::CSS_CLASS() => 'mrslink',
1029             },
1030             );
1031             while (my $record = $find->next) {
1032             print join ("\n", @$record) . "\n";
1033              
1034             Which prints something like:
1035              
1036             8618
1037             Eukaryota
1038             ...
1039             Disulfide bond
1040             ...
1041             92332489
1042             ...
1043            
1044              
1045             =back
1046              
1047             =head3 count
1048              
1049             It returns a number of entries in the whole databank.
1050              
1051             print $client->db ('enzyme')->count;
1052             4645
1053              
1054             Do not confuse it with the method of the same name but called on the
1055             object returned by the I method - that one returns a number of
1056             hits of that particular query.
1057              
1058             =head3 entry
1059              
1060             It takes an entry ID (mandatory), and optionally its format and
1061             extended format, and it returns the given entry:
1062              
1063             print $client->db ('enzyme')->entry ('3.4.21.60');
1064             ID 3.4.21.60
1065             DE Scutelarin.
1066             AN Taipan activator.
1067             CA Selective cleavage of Arg-|-Thr and Arg-|-Ile in prothrombin to form
1068             CA thrombin and two inactive fragments.
1069             CC -!- From the venom of Taipan snake (Oxyuranus scutellatus).
1070             CC -!- Converts prothrombin to thrombin in the absence of coagulation factor
1071             CC Va, and is potentiated by phospholipid and calcium.
1072             CC -!- Specificity is similar to that of factor Xa.
1073             CC -!- Binds calcium via gamma-carboxyglutamic acid residues.
1074             CC -!- Similar enzymes are known from the venom of other Australian elapid
1075             CC snakes Pseudonaja textilis, Oxyuranus microlepidotus and Demansia
1076             CC nuchalis affinis.
1077             CC -!- Formerly EC 3.4.99.28.
1078             //
1079              
1080             print $client->db ('enzyme')->entry ('3.4.21.60',
1081             MRS::EntryFormat->TITLE);
1082             Scutelarin.
1083              
1084             The optional C is a hashref and it was explained
1085             earlier in the section about the C method.
1086              
1087             =head3 id, name, version, blastable, url, script, files, indices, aliases
1088              
1089             There are several methods delivering databank properties. They have no
1090             arguments:
1091              
1092             my $db = $client->db('omim');
1093             print $db->id . "\n";
1094             print $db->name . "\n";
1095             print $db->version . "\n";
1096             print $db->blastable . "\n";
1097             print $db->url . "\n";
1098             print $db->script . "\n";
1099             print $db->aliases . "\n";
1100              
1101             =head3 files
1102              
1103             Each databank consists of one or more files. This method returns a
1104             reference to an array of C
1105             instances. Each such instance has properties reachable by the
1106             following "getters" methods:
1107              
1108             sub say { print @_, "\n"; }
1109              
1110             my $db_files = $client->db('uniprot')->files;
1111             foreach my $file (@{ $db_files }) {
1112             say $file->id;
1113             say $file->version;
1114             say $file->last_modified;
1115             say $file->entries_count;
1116             say $file->raw_data_size;
1117             say $file->file_size;
1118             say '';
1119             }
1120              
1121             =head3 indices
1122              
1123             Each databank is indexed by (usually several) indices. This method
1124             returns a reference to an array of C
1125             instances. Each such instance has properties reachable by the
1126             "getters" method:
1127              
1128             my $db_indices = $client->db('uniprot')->indices;
1129             foreach my $idx (@{ $db_indices }) {
1130             printf ("%-15s%-15s%9d %-9s %s\n",
1131             $idx->db,
1132             $idx->id,
1133             $idx->count,
1134             $idx->type,
1135             $idx->description);
1136             }
1137              
1138             The index I is important because it can be used in the
1139             queries. For example, assuming that the database has an index I
1140             (organism species):
1141              
1142             $db->find (query => 'rds AND os:human');
1143              
1144             =head2 MRS::Client::Find
1145              
1146             This object carries results of a query; it is returned by the I
1147             method, called either on a databank instance or on the whole
1148             client. Actually, in case of the whole client, the returned type is of
1149             type C which is a subclass
1150             C.
1151              
1152             =head3 db, terms, query, all_terms_required, max_entries
1153              
1154             The getter methods just reflect query arguments (the ones given to the
1155             C method):
1156              
1157             sub say { print @_, "\n"; }
1158              
1159             my $find = $client->db('uniprot')->find('sapiens');
1160             say $find->db;
1161             say join (", ", @ {$find->terms });
1162             say $find->query;
1163             say $find->max_entries;
1164             say $find->all_terms_required;
1165              
1166             The I (a ref array) are either from the I or I
1167             argument, and the I is 1 (when terms are coming
1168             from the I) or zero.
1169              
1170             =head3 count
1171              
1172             Finally, you can get the number of hits of this query. Be aware (as
1173             mentioned elsewhere in this document) that boolean queries return only
1174             an estimate, usually much higher than is the reality.
1175              
1176             =head2 MRS::Client::MultiFind
1177              
1178             This object is returned from the C method made to all
1179             databanks. It is a subclass of the C with one
1180             additional method:
1181              
1182             =head3 db_counts
1183              
1184             It returns databank names and their total counts in a hash (not a
1185             reference) where keys are the databank names and values the entry
1186             counts:
1187              
1188             my %counts = $find->db_counts;
1189             foreach my $db (sort keys %counts) {
1190             printf ("%-15s %9d\n", $db, $counts{$db});
1191             }
1192              
1193             =head2 MRS::Client::Hit
1194              
1195             Finally, a tiny object representing a hit, a result of a query before
1196             going to a databank for the full contents of a found entry. It
1197             contains the databank's ID (where the hit was found), the score that
1198             this hit achieved (for boolean queries, the score is always 1) and the
1199             ID and title of the entry represented by this hit.
1200              
1201             The corresponding getters methods are I, I, I and
1202             I. </td> </tr> <tr> <td class="h" > <a name="1203">1203</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1204">1204</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> The I<next> method (as shown above) returns just hits (instead of the </td> </tr> <tr> <td class="h" > <a name="1205">1205</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> full entries) when the format I<MRS::EntryFormat->HEADER> is </td> </tr> <tr> <td class="h" > <a name="1206">1206</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> specified. </td> </tr> <tr> <td class="h" > <a name="1207">1207</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1208">1208</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =head2 MRS::Client::Blast </td> </tr> <tr> <td class="h" > <a name="1209">1209</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1210">1210</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> The MRS servers provide sequence homology searches, the famous Blast </td> </tr> <tr> <td class="h" > <a name="1211">1211</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> program (namely the I<blastp> program for protein sequences). An input </td> </tr> <tr> <td class="h" > <a name="1212">1212</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> sequence (in FASTA format) is searched against one of the MRS </td> </tr> <tr> <td class="h" > <a name="1213">1213</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> databanks. It can be any MRS databank whose method C<blastable> </td> </tr> <tr> <td class="h" > <a name="1214">1214</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> returns true (e.g. uniprot). An input sequence and a databank are the </td> </tr> <tr> <td class="h" > <a name="1215">1215</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> only mandatory input parameters. Other common Blast parameters are </td> </tr> <tr> <td class="h" > <a name="1216">1216</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> also supported. </td> </tr> <tr> <td class="h" > <a name="1217">1217</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1218">1218</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> The invocation is asynchronous. It means that the I<run> method </td> </tr> <tr> <td class="h" > <a name="1219">1219</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> returns immediately, without waiting for the Blast program to finish, </td> </tr> <tr> <td class="h" > <a name="1220">1220</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> giving back a I<job id>, a handler that can be used later for polling </td> </tr> <tr> <td class="h" > <a name="1221">1221</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> for status, and, once status indicates the Blast finishes, for getting </td> </tr> <tr> <td class="h" > <a name="1222">1222</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> results (or an error message). This is the typical usage: </td> </tr> <tr> <td class="h" > <a name="1223">1223</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1224">1224</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> my @run_args = (fasta_file => '...', db => '...', ...); </td> </tr> <tr> <td class="h" > <a name="1225">1225</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> my $job = $client->blast->run (@run_args); </td> </tr> <tr> <td class="h" > <a name="1226">1226</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> sleep 10 while (not $job->completed); </td> </tr> <tr> <td class="h" > <a name="1227">1227</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> print $job->error if $job->failed; </td> </tr> <tr> <td class="h" > <a name="1228">1228</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> print $job->results; </td> </tr> <tr> <td class="h" > <a name="1229">1229</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1230">1230</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> 529.0 1.346582e-149 [vsph_trije ] 1 Snake venom serine protease homolog; </td> </tr> <tr> <td class="h" > <a name="1231">1231</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> 509.0 1.411994e-143 [vspa_triga ] 1 Venom serine proteinase 2A; </td> </tr> <tr> <td class="h" > <a name="1232">1232</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> 508.0 2.823987e-143 [vsp1m_trist ] 1 Venom serine protease 1 homolog; </td> </tr> <tr> <td class="h" > <a name="1233">1233</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> 506.0 1.129595e-142 [vsp07_trist ] 1 Venom serine protease KN7 homolog; </td> </tr> <tr> <td class="h" > <a name="1234">1234</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> 488.0 2.961165e-137 [vsp2_trifl ] 1 Venom serine proteinase 2; </td> </tr> <tr> <td class="h" > <a name="1235">1235</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> 487.0 5.922331e-137 [vsp1_trije ] 1 Venom serine proteinase-like protein; </td> </tr> <tr> <td class="h" > <a name="1236">1236</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> 456.0 1.271811e-127 [vsp04_trist ] 1 Venom serine protease KN4 homolog; </td> </tr> <tr> <td class="h" > <a name="1237">1237</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> ... </td> </tr> <tr> <td class="h" > <a name="1238">1238</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1239">1239</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> You can also use provided script C<mrsblast> that polls for you (if </td> </tr> <tr> <td class="h" > <a name="1240">1240</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> you wish so). </td> </tr> <tr> <td class="h" > <a name="1241">1241</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1242">1242</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> In order to create an C<MRS::Client::Blast> instance, use the factory method: </td> </tr> <tr> <td class="h" > <a name="1243">1243</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1244">1244</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> my $blast = $client->blast; </td> </tr> <tr> <td class="h" > <a name="1245">1245</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1246">1246</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =head3 run </td> </tr> <tr> <td class="h" > <a name="1247">1247</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1248">1248</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> The main method that starts Blast with the given parameters and </td> </tr> <tr> <td class="h" > <a name="1249">1249</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> immediately returns an object C<MRS::Client::Blast::Job> that can be </td> </tr> <tr> <td class="h" > <a name="1250">1250</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> used for all other important methods. If you plan to stop your Perl </td> </tr> <tr> <td class="h" > <a name="1251">1251</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> program and start it again later, you need to remember the job ID: </td> </tr> <tr> <td class="h" > <a name="1252">1252</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1253">1253</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> my $job = $blast->run (...); </td> </tr> <tr> <td class="h" > <a name="1254">1254</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> print $job->id; </td> </tr> <tr> <td class="h" > <a name="1255">1255</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1256">1256</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> The job ID can be later used to re-create the same (well, similar) Job </td> </tr> <tr> <td class="h" > <a name="1257">1257</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> object (see method I<job> below) that again provides all important </td> </tr> <tr> <td class="h" > <a name="1258">1258</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> methods (such as getting results). </td> </tr> <tr> <td class="h" > <a name="1259">1259</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1260">1260</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> The method I<run> has following arguments (the Job object has the same </td> </tr> <tr> <td class="h" > <a name="1261">1261</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> "getter" methods), all given as a hash: </td> </tr> <tr> <td class="h" > <a name="1262">1262</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1263">1263</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =over </td> </tr> <tr> <td class="h" > <a name="1264">1264</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1265">1265</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item db </td> </tr> <tr> <td class="h" > <a name="1266">1266</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1267">1267</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> An MRS databank to search against. Mandatory parameter. </td> </tr> <tr> <td class="h" > <a name="1268">1268</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1269">1269</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item fasta </td> </tr> <tr> <td class="h" > <a name="1270">1270</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1271">1271</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> A protein sequence in a FASTA format. Mandatory parameter unless </td> </tr> <tr> <td class="h" > <a name="1272">1272</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> C<fasta_file> is given. </td> </tr> <tr> <td class="h" > <a name="1273">1273</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1274">1274</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item fasta_file </td> </tr> <tr> <td class="h" > <a name="1275">1275</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1276">1276</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> A name of a file containing a protein sequence in a FASTA </td> </tr> <tr> <td class="h" > <a name="1277">1277</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> format. Mandatory parameter unless C<fasta> is given. </td> </tr> <tr> <td class="h" > <a name="1278">1278</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1279">1279</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item filter </td> </tr> <tr> <td class="h" > <a name="1280">1280</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1281">1281</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Low complexity filter. Boolean parameter. Default is 1. </td> </tr> <tr> <td class="h" > <a name="1282">1282</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1283">1283</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item expect </td> </tr> <tr> <td class="h" > <a name="1284">1284</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1285">1285</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> E-value cutoff. A float value. Default is 10.0. </td> </tr> <tr> <td class="h" > <a name="1286">1286</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1287">1287</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item word_size </td> </tr> <tr> <td class="h" > <a name="1288">1288</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1289">1289</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> An integer. Default is 3. </td> </tr> <tr> <td class="h" > <a name="1290">1290</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1291">1291</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item matrix </td> </tr> <tr> <td class="h" > <a name="1292">1292</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1293">1293</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Scoring matrix. Default BLOSUM62. </td> </tr> <tr> <td class="h" > <a name="1294">1294</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1295">1295</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item open_cost </td> </tr> <tr> <td class="h" > <a name="1296">1296</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1297">1297</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Gap opening penalty. An integer. Default is 11. </td> </tr> <tr> <td class="h" > <a name="1298">1298</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1299">1299</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item extend_cost </td> </tr> <tr> <td class="h" > <a name="1300">1300</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1301">1301</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Gap extension penalty. Default is 1. </td> </tr> <tr> <td class="h" > <a name="1302">1302</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1303">1303</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item query </td> </tr> <tr> <td class="h" > <a name="1304">1304</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1305">1305</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> An MRS boolean query to limit the search space. </td> </tr> <tr> <td class="h" > <a name="1306">1306</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1307">1307</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item gapped </td> </tr> <tr> <td class="h" > <a name="1308">1308</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1309">1309</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> A boolean parameter. Its true value performs gapped alignment. Default </td> </tr> <tr> <td class="h" > <a name="1310">1310</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> is true. </td> </tr> <tr> <td class="h" > <a name="1311">1311</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1312">1312</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item max_hits </td> </tr> <tr> <td class="h" > <a name="1313">1313</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1314">1314</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Limit reported hits. An integer. Default is 250. </td> </tr> <tr> <td class="h" > <a name="1315">1315</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1316">1316</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =back </td> </tr> <tr> <td class="h" > <a name="1317">1317</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1318">1318</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =head3 job </td> </tr> <tr> <td class="h" > <a name="1319">1319</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1320">1320</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> The method finds or re-creates a Job object of the given ID: </td> </tr> <tr> <td class="h" > <a name="1321">1321</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1322">1322</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> my $job = $client->blast->job ('0f37a544-a7a2-4239-b950-65a6aa07d1ef'); </td> </tr> <tr> <td class="h" > <a name="1323">1323</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> print $job->id; </td> </tr> <tr> <td class="h" > <a name="1324">1324</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> print $job->status; </td> </tr> <tr> <td class="h" > <a name="1325">1325</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1326">1326</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> It dies with an error if such Job is not known to the MRS server. </td> </tr> <tr> <td class="h" > <a name="1327">1327</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1328">1328</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> The returned Job object can be used to ask for the Job status, or for </td> </tr> <tr> <td class="h" > <a name="1329">1329</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> getting the Job results. There is one caveat, however. The re-created </td> </tr> <tr> <td class="h" > <a name="1330">1330</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Job object is not that "rich" as was its original version: it does not </td> </tr> <tr> <td class="h" > <a name="1331">1331</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> know, for example, what parameters were used to start this blast </td> </tr> <tr> <td class="h" > <a name="1332">1332</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> job. Unfortunately, the MRS server keeps only the Job ID and nothing </td> </tr> <tr> <td class="h" > <a name="1333">1333</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> else. Fortunately, the parameters are needed only for the results in </td> </tr> <tr> <td class="h" > <a name="1334">1334</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> the XML format (see more about available formats below, in the method </td> </tr> <tr> <td class="h" > <a name="1335">1335</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> I<$job-E<gt>results>) - and you can add them (if you still have them), as a </td> </tr> <tr> <td class="h" > <a name="1336">1336</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> hash, to the C<job> method when re-creating a new Job instance: </td> </tr> <tr> <td class="h" > <a name="1337">1337</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1338">1338</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> my $job - $client->blast->job ('0f37a544-a7a2-4239-b950-65a6aa07d1ef', </td> </tr> <tr> <td class="h" > <a name="1339">1339</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> fasta => '...', </td> </tr> <tr> <td class="h" > <a name="1340">1340</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> db => 'iniprot', ...); </td> </tr> <tr> <td class="h" > <a name="1341">1341</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1342">1342</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =head2 MRS::Client::Blast::Job </td> </tr> <tr> <td class="h" > <a name="1343">1343</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1344">1344</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> The Job object represents a single Blast invocation with a set of </td> </tr> <tr> <td class="h" > <a name="1345">1345</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> input parameters and, later, with results. It is also used to poll for </td> </tr> <tr> <td class="h" > <a name="1346">1346</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> the status of the running job. Instances of this objects are created </td> </tr> <tr> <td class="h" > <a name="1347">1347</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> by the I<run> or I<job> methods of the C<blast> object. The Job's </td> </tr> <tr> <td class="h" > <a name="1348">1348</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> methods are: </td> </tr> <tr> <td class="h" > <a name="1349">1349</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1350">1350</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =over </td> </tr> <tr> <td class="h" > <a name="1351">1351</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1352">1352</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item id </td> </tr> <tr> <td class="h" > <a name="1353">1353</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1354">1354</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Job ID, an important handler if you have to re-create an </td> </tr> <tr> <td class="h" > <a name="1355">1355</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> C<MRS::Client::Blast::Job> object. </td> </tr> <tr> <td class="h" > <a name="1356">1356</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1357">1357</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item "getter" methods </td> </tr> <tr> <td class="h" > <a name="1358">1358</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1359">1359</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> All these methods are equivalent to (and named the same as) the </td> </tr> <tr> <td class="h" > <a name="1360">1360</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> parameters given to the C<run> method (described above): </td> </tr> <tr> <td class="h" > <a name="1361">1361</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1362">1362</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =over </td> </tr> <tr> <td class="h" > <a name="1363">1363</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1364">1364</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item db </td> </tr> <tr> <td class="h" > <a name="1365">1365</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1366">1366</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item fasta </td> </tr> <tr> <td class="h" > <a name="1367">1367</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1368">1368</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item fasta_file </td> </tr> <tr> <td class="h" > <a name="1369">1369</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1370">1370</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item filter </td> </tr> <tr> <td class="h" > <a name="1371">1371</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1372">1372</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item expect </td> </tr> <tr> <td class="h" > <a name="1373">1373</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1374">1374</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item word_size </td> </tr> <tr> <td class="h" > <a name="1375">1375</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1376">1376</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item matrix </td> </tr> <tr> <td class="h" > <a name="1377">1377</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1378">1378</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item open_cost </td> </tr> <tr> <td class="h" > <a name="1379">1379</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1380">1380</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item extend_cost </td> </tr> <tr> <td class="h" > <a name="1381">1381</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1382">1382</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item query </td> </tr> <tr> <td class="h" > <a name="1383">1383</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1384">1384</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item max_hits </td> </tr> <tr> <td class="h" > <a name="1385">1385</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1386">1386</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item gapped </td> </tr> <tr> <td class="h" > <a name="1387">1387</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1388">1388</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item </td> </tr> <tr> <td class="h" > <a name="1389">1389</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1390">1390</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =back </td> </tr> <tr> <td class="h" > <a name="1391">1391</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1392">1392</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item status, completed, failed </td> </tr> <tr> <td class="h" > <a name="1393">1393</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1394">1394</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> The I<status> returns one of the C<MRS::JobStatus>: </td> </tr> <tr> <td class="h" > <a name="1395">1395</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1396">1396</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> use constant { </td> </tr> <tr> <td class="h" > <a name="1397">1397</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> UNKNOWN => 'unknown', </td> </tr> <tr> <td class="h" > <a name="1398">1398</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> QUEUED => 'queued', </td> </tr> <tr> <td class="h" > <a name="1399">1399</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> RUNNING => 'running', </td> </tr> <tr> <td class="h" > <a name="1400">1400</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> ERROR => 'error', </td> </tr> <tr> <td class="h" > <a name="1401">1401</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> FINISHED => 'finished', </td> </tr> <tr> <td class="h" > <a name="1402">1402</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> }; </td> </tr> <tr> <td class="h" > <a name="1403">1403</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1404">1404</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> The I<completed> returns true if the status is either C<ERROR> or </td> </tr> <tr> <td class="h" > <a name="1405">1405</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> C<FINISHED>. The I<failed> returns true if the status is </td> </tr> <tr> <td class="h" > <a name="1406">1406</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> C<ERROR>. Typical usage for polling a running job is: </td> </tr> <tr> <td class="h" > <a name="1407">1407</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1408">1408</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> sleep 10 while (not $job->completed); </td> </tr> <tr> <td class="h" > <a name="1409">1409</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1410">1410</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item error </td> </tr> <tr> <td class="h" > <a name="1411">1411</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1412">1412</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> It returns an error message, or undef if the status is not </td> </tr> <tr> <td class="h" > <a name="1413">1413</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> C<ERROR>. Typical usage is: </td> </tr> <tr> <td class="h" > <a name="1414">1414</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1415">1415</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> print $job->error if $job->failed; </td> </tr> <tr> <td class="h" > <a name="1416">1416</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1417">1417</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item results </td> </tr> <tr> <td class="h" > <a name="1418">1418</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1419">1419</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Finally, the more interesting method. It returns an object of type </td> </tr> <tr> <td class="h" > <a name="1420">1420</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> C<MRS::Client::Blast::Result> that can be either used on its own (see </td> </tr> <tr> <td class="h" > <a name="1421">1421</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> its "getter" method below), or converted to strings of one of the </td> </tr> <tr> <td class="h" > <a name="1422">1422</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> format predefined in C<MRS::BlastOutputFormat>: </td> </tr> <tr> <td class="h" > <a name="1423">1423</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1424">1424</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> use constant { </td> </tr> <tr> <td class="h" > <a name="1425">1425</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> XML => 'xml', </td> </tr> <tr> <td class="h" > <a name="1426">1426</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> HITS => 'hits', </td> </tr> <tr> <td class="h" > <a name="1427">1427</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> FULL => 'full', </td> </tr> <tr> <td class="h" > <a name="1428">1428</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> STATS => 'stats', </td> </tr> <tr> <td class="h" > <a name="1429">1429</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> }; </td> </tr> <tr> <td class="h" > <a name="1430">1430</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1431">1431</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> The format is the only parameter of this method. Default format is </td> </tr> <tr> <td class="h" > <a name="1432">1432</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> C<HITS>. The conversion to the given format is done by overloading the </td> </tr> <tr> <td class="h" > <a name="1433">1433</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> double quotes operator, calling internally the method "as_string". You </td> </tr> <tr> <td class="h" > <a name="1434">1434</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> just print the object: </td> </tr> <tr> <td class="h" > <a name="1435">1435</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1436">1436</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> print $job->results; </td> </tr> <tr> <td class="h" > <a name="1437">1437</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1438">1438</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> 447.0 6.511672e-125 [vspgl_glosh ] 1 Thrombin-like enzyme gloshedobin; </td> </tr> <tr> <td class="h" > <a name="1439">1439</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> 429.0 1.706996e-119 [vsp2_viple ] 1 Venom serine proteinase-like protein 2; </td> </tr> <tr> <td class="h" > <a name="1440">1440</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> 421.0 4.369909e-117 [vsp12_trist ] 1 Venom serine protease KN12; </td> </tr> <tr> <td class="h" > <a name="1441">1441</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> 419.0 1.747964e-116 [vsps1_trist ] 1 Thrombin-like enzyme stejnefibrase-1; </td> </tr> <tr> <td class="h" > <a name="1442">1442</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> ... </td> </tr> <tr> <td class="h" > <a name="1443">1443</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1444">1444</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Where lines are individual hits and columns are: I<bit_score>, </td> </tr> <tr> <td class="h" > <a name="1445">1445</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> I<expect>, sequence ID, number of HSPs for this hit, sequence </td> </tr> <tr> <td class="h" > <a name="1446">1446</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> description. </td> </tr> <tr> <td class="h" > <a name="1447">1447</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1448">1448</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Or, giving just the Blast run statistics: </td> </tr> <tr> <td class="h" > <a name="1449">1449</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1450">1450</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> print $job->results (MRS::BlastOutputFormat->STATS); </td> </tr> <tr> <td class="h" > <a name="1451">1451</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1452">1452</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> DB count: 514212 </td> </tr> <tr> <td class="h" > <a name="1453">1453</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> DB length: 180900945 </td> </tr> <tr> <td class="h" > <a name="1454">1454</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Search space: 23664675636 </td> </tr> <tr> <td class="h" > <a name="1455">1455</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Kappa: 0.041 </td> </tr> <tr> <td class="h" > <a name="1456">1456</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Lambda: 0.267 </td> </tr> <tr> <td class="h" > <a name="1457">1457</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Entropy: 0.140 </td> </tr> <tr> <td class="h" > <a name="1458">1458</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1459">1459</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Or, showing everything (in a rather un-parsable form, useful more for </td> </tr> <tr> <td class="h" > <a name="1460">1460</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> testing than anything else): </td> </tr> <tr> <td class="h" > <a name="1461">1461</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1462">1462</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> print $job->results (MRS::BlastOutputFormat->FULL); </td> </tr> <tr> <td class="h" > <a name="1463">1463</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1464">1464</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Or, in an XML format: </td> </tr> <tr> <td class="h" > <a name="1465">1465</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1466">1466</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> print $job->results (MRS::BlastOutputFormat->XML); </td> </tr> <tr> <td class="h" > <a name="1467">1467</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1468">1468</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =back </td> </tr> <tr> <td class="h" > <a name="1469">1469</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1470">1470</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =head2 MRS::Client::Blast::Result </td> </tr> <tr> <td class="h" > <a name="1471">1471</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1472">1472</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> You can explore the returned Blast results by the following "getter" </td> </tr> <tr> <td class="h" > <a name="1473">1473</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> methods - going from the whole result to the individual hits and </td> </tr> <tr> <td class="h" > <a name="1474">1474</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> inside hits to the individual HSPs (High-scoring pairs): </td> </tr> <tr> <td class="h" > <a name="1475">1475</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1476">1476</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =over </td> </tr> <tr> <td class="h" > <a name="1477">1477</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1478">1478</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item db_count </td> </tr> <tr> <td class="h" > <a name="1479">1479</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1480">1480</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item db_length </td> </tr> <tr> <td class="h" > <a name="1481">1481</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1482">1482</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item db_space </td> </tr> <tr> <td class="h" > <a name="1483">1483</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1484">1484</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Effective search space. </td> </tr> <tr> <td class="h" > <a name="1485">1485</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1486">1486</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item kappa </td> </tr> <tr> <td class="h" > <a name="1487">1487</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1488">1488</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item lambda </td> </tr> <tr> <td class="h" > <a name="1489">1489</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1490">1490</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item entropy </td> </tr> <tr> <td class="h" > <a name="1491">1491</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1492">1492</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item hits </td> </tr> <tr> <td class="h" > <a name="1493">1493</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1494">1494</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> It returns a reference to an array of C<MRS::Client::Blast::Hit>s </td> </tr> <tr> <td class="h" > <a name="1495">1495</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> where each hit has methods: </td> </tr> <tr> <td class="h" > <a name="1496">1496</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1497">1497</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =over </td> </tr> <tr> <td class="h" > <a name="1498">1498</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1499">1499</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item id </td> </tr> <tr> <td class="h" > <a name="1500">1500</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1501">1501</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item title </td> </tr> <tr> <td class="h" > <a name="1502">1502</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1503">1503</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item sequences </td> </tr> <tr> <td class="h" > <a name="1504">1504</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1505">1505</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> It is a reference to an array of sequence IDs. </td> </tr> <tr> <td class="h" > <a name="1506">1506</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1507">1507</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item hsps </td> </tr> <tr> <td class="h" > <a name="1508">1508</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1509">1509</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> It is a reference to an array of C<MRS::Client::Blast::HSP>s </td> </tr> <tr> <td class="h" > <a name="1510">1510</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> where each HSP has methods: </td> </tr> <tr> <td class="h" > <a name="1511">1511</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1512">1512</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =over </td> </tr> <tr> <td class="h" > <a name="1513">1513</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1514">1514</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item score </td> </tr> <tr> <td class="h" > <a name="1515">1515</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1516">1516</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item bit_score </td> </tr> <tr> <td class="h" > <a name="1517">1517</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1518">1518</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item expect </td> </tr> <tr> <td class="h" > <a name="1519">1519</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1520">1520</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item query_start </td> </tr> <tr> <td class="h" > <a name="1521">1521</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1522">1522</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item subject_start </td> </tr> <tr> <td class="h" > <a name="1523">1523</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1524">1524</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item identity </td> </tr> <tr> <td class="h" > <a name="1525">1525</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1526">1526</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item positive </td> </tr> <tr> <td class="h" > <a name="1527">1527</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1528">1528</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item gaps </td> </tr> <tr> <td class="h" > <a name="1529">1529</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1530">1530</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item subject_length </td> </tr> <tr> <td class="h" > <a name="1531">1531</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1532">1532</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item query_align </td> </tr> <tr> <td class="h" > <a name="1533">1533</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1534">1534</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item subject_align </td> </tr> <tr> <td class="h" > <a name="1535">1535</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1536">1536</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item midline </td> </tr> <tr> <td class="h" > <a name="1537">1537</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1538">1538</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =back </td> </tr> <tr> <td class="h" > <a name="1539">1539</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1540">1540</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =back </td> </tr> <tr> <td class="h" > <a name="1541">1541</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1542">1542</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =back </td> </tr> <tr> <td class="h" > <a name="1543">1543</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1544">1544</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Try to explore various result formats by using the provided script </td> </tr> <tr> <td class="h" > <a name="1545">1545</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> C<mrsblast>. This waits for a job to be completed and then prints its </td> </tr> <tr> <td class="h" > <a name="1546">1546</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> hits: </td> </tr> <tr> <td class="h" > <a name="1547">1547</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1548">1548</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> mrsblast -d sprot -i 'your.fasta' </td> </tr> <tr> <td class="h" > <a name="1549">1549</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1550">1550</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> This shows Blast statistics: </td> </tr> <tr> <td class="h" > <a name="1551">1551</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1552">1552</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> mrsblast -d sprot -i 'your.fasta' -N </td> </tr> <tr> <td class="h" > <a name="1553">1553</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1554">1554</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> This produces an XML output to a given file: </td> </tr> <tr> <td class="h" > <a name="1555">1555</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1556">1556</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> mrsblast -d sprot -i 'your.fasta' -x results.xml </td> </tr> <tr> <td class="h" > <a name="1557">1557</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1558">1558</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Finally, this gives a long listing with all details: </td> </tr> <tr> <td class="h" > <a name="1559">1559</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1560">1560</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> mrsblast -d sprot -i 'your.fasta' -f </td> </tr> <tr> <td class="h" > <a name="1561">1561</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1562">1562</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =head2 MRS::Client::Clustal </td> </tr> <tr> <td class="h" > <a name="1563">1563</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1564">1564</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> B<Attention:> This module is used only by MRS version 5, </td> </tr> <tr> <td class="h" > <a name="1565">1565</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> See L<MRS VERSIONS> for details. </td> </tr> <tr> <td class="h" > <a name="1566">1566</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1567">1567</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> The module wrapping the multiple alignment program I<clustalw>. The </td> </tr> <tr> <td class="h" > <a name="1568">1568</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> program is optional and, therefore, not all MRS servers may have </td> </tr> <tr> <td class="h" > <a name="1569">1569</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> it. Use the factory method for creating instances of </td> </tr> <tr> <td class="h" > <a name="1570">1570</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> F<MRS::Client::Clustal>: </td> </tr> <tr> <td class="h" > <a name="1571">1571</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1572">1572</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> $client->clustal </td> </tr> <tr> <td class="h" > <a name="1573">1573</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1574">1574</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =head3 run </td> </tr> <tr> <td class="h" > <a name="1575">1575</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1576">1576</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> The main method, invoking I<clustalw> with mandatory input sequences </td> </tr> <tr> <td class="h" > <a name="1577">1577</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> and optionally a couple of other parameters: </td> </tr> <tr> <td class="h" > <a name="1578">1578</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1579">1579</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> my $result = $client->clustal->run (fasta_file => 'my.proteins.fasta'); </td> </tr> <tr> <td class="h" > <a name="1580">1580</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1581">1581</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =over </td> </tr> <tr> <td class="h" > <a name="1582">1582</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1583">1583</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item fasta_file </td> </tr> <tr> <td class="h" > <a name="1584">1584</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1585">1585</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> A file with multiple sequences in FASTA format. </td> </tr> <tr> <td class="h" > <a name="1586">1586</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1587">1587</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item open_cost </td> </tr> <tr> <td class="h" > <a name="1588">1588</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1589">1589</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> A gap opening penalty (an integer). </td> </tr> <tr> <td class="h" > <a name="1590">1590</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1591">1591</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item extend_cost </td> </tr> <tr> <td class="h" > <a name="1592">1592</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1593">1593</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> A gap extension penalty (a float). </td> </tr> <tr> <td class="h" > <a name="1594">1594</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1595">1595</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =back </td> </tr> <tr> <td class="h" > <a name="1596">1596</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1597">1597</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> It returns result in an instance of F<MRS::Client::Clustal::Result>. </td> </tr> <tr> <td class="h" > <a name="1598">1598</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1599">1599</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =head3 open_cost </td> </tr> <tr> <td class="h" > <a name="1600">1600</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1601">1601</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> It returns what gap opening penalty has been set in the I<run> method. </td> </tr> <tr> <td class="h" > <a name="1602">1602</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1603">1603</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =head3 extend_cost </td> </tr> <tr> <td class="h" > <a name="1604">1604</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1605">1605</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> It returns what gap extension penalty has been set in the I<run> method. </td> </tr> <tr> <td class="h" > <a name="1606">1606</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1607">1607</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =head2 MRS::Client::Clustal::Result </td> </tr> <tr> <td class="h" > <a name="1608">1608</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1609">1609</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> It is created by running: </td> </tr> <tr> <td class="h" > <a name="1610">1610</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1611">1611</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> $client->clustal->run (...); </td> </tr> <tr> <td class="h" > <a name="1612">1612</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1613">1613</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =head3 alignment </td> </tr> <tr> <td class="h" > <a name="1614">1614</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1615">1615</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> It returns a reference to an array of </td> </tr> <tr> <td class="h" > <a name="1616">1616</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> F<MRS::Client::Clustal::Sequence> instances. Each of them has methods </td> </tr> <tr> <td class="h" > <a name="1617">1617</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> I<id> and I<sequence>. You can also just print the formatted alignment </td> </tr> <tr> <td class="h" > <a name="1618">1618</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> (it uses its own I<as_string> method that overloads double quotes </td> </tr> <tr> <td class="h" > <a name="1619">1619</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> operator): </td> </tr> <tr> <td class="h" > <a name="1620">1620</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1621">1621</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> print $client->clustal->run (fasta_file => 'several.proteins.fasta'); </td> </tr> <tr> <td class="h" > <a name="1622">1622</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1623">1623</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> vsph_trije : -VMGWGTISATKETHPDVPYCANINILDYSVCRAAYARLPATSRTLCAGILE-----GGKDSCLTD----SGGPLICNGQFQGIVSWGGHPCGQP-RKPGLYTKVFDHLDWIKSIIAGNKDATCPP </td> </tr> <tr> <td class="h" > <a name="1624">1624</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> nxsa_latse : ----MKTLLLTLVVVTIV--CLDLGYTR--ICFNHQSSQPQTTKT-CS---------PGESSCYNK----QWS------DFRGTIIERG--CGCPTVKPGI------KLSCCESEVCNN------- </td> </tr> <tr> <td class="h" > <a name="1625">1625</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> pa21b_pseau: NLIQFGNMIQCANKGSRP--SLDYADYG-CYCGWGGSGTPVDELDRCCQVHDNCYEQAGKKGCFPKLTLYSWKCTGNVPTCNSKPGCKSFVCACDAAAAKC----FAKAPYKKENYNIDTKKRCK- </td> </tr> <tr> <td class="h" > <a name="1626">1626</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1627">1627</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =head3 diagnostics </td> </tr> <tr> <td class="h" > <a name="1628">1628</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1629">1629</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> It shows the standard output of the underlying F<clustalw> program: </td> </tr> <tr> <td class="h" > <a name="1630">1630</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1631">1631</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> my $result = $client->clustal->run (fasta_file => 'several.proteins.fasta'); </td> </tr> <tr> <td class="h" > <a name="1632">1632</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> print $result->diagnostics; </td> </tr> <tr> <td class="h" > <a name="1633">1633</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1634">1634</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> CLUSTAL 2.0.10 Multiple Sequence Alignments </td> </tr> <tr> <td class="h" > <a name="1635">1635</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1636">1636</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Sequence type explicitly set to Protein </td> </tr> <tr> <td class="h" > <a name="1637">1637</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Sequence format is Pearson </td> </tr> <tr> <td class="h" > <a name="1638">1638</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Sequence 1: vsph_trije 115 aa </td> </tr> <tr> <td class="h" > <a name="1639">1639</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Sequence 2: nxsa_latse 83 aa </td> </tr> <tr> <td class="h" > <a name="1640">1640</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Sequence 3: pa21b_pseau 118 aa </td> </tr> <tr> <td class="h" > <a name="1641">1641</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Start of Pairwise alignments </td> </tr> <tr> <td class="h" > <a name="1642">1642</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Aligning... </td> </tr> <tr> <td class="h" > <a name="1643">1643</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1644">1644</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Sequences (1:2) Aligned. Score: 13 </td> </tr> <tr> <td class="h" > <a name="1645">1645</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Sequences (1:3) Aligned. Score: 5 </td> </tr> <tr> <td class="h" > <a name="1646">1646</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Sequences (2:3) Aligned. Score: 8 </td> </tr> <tr> <td class="h" > <a name="1647">1647</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Guide tree file created: ... </td> </tr> <tr> <td class="h" > <a name="1648">1648</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1649">1649</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> There are 2 groups </td> </tr> <tr> <td class="h" > <a name="1650">1650</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Start of Multiple Alignment </td> </tr> <tr> <td class="h" > <a name="1651">1651</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1652">1652</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Aligning... </td> </tr> <tr> <td class="h" > <a name="1653">1653</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Group 1: Delayed </td> </tr> <tr> <td class="h" > <a name="1654">1654</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Group 2: Delayed </td> </tr> <tr> <td class="h" > <a name="1655">1655</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Alignment Score -93 </td> </tr> <tr> <td class="h" > <a name="1656">1656</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1657">1657</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> GDE-Alignment file created ... </td> </tr> <tr> <td class="h" > <a name="1658">1658</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1659">1659</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =head3 failed </td> </tr> <tr> <td class="h" > <a name="1660">1660</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1661">1661</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> It returns standard error output of the underlying F<clustalw> </td> </tr> <tr> <td class="h" > <a name="1662">1662</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> program. It the program finished without problems, it returns undef. </td> </tr> <tr> <td class="h" > <a name="1663">1663</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1664">1664</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =head1 MRS VERSIONS </td> </tr> <tr> <td class="h" > <a name="1665">1665</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1666">1666</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> The SOAP API of the MRS server slightly (or significantly, depending </td> </tr> <tr> <td class="h" > <a name="1667">1667</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> on what you were using) changed between version 5 and 6 (the version </td> </tr> <tr> <td class="h" > <a name="1668">1668</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> numbers indicate the MRS server version, not the version of the </td> </tr> <tr> <td class="h" > <a name="1669">1669</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> C<MRS::Client> module). The C<MRS::Client> module can work with both </td> </tr> <tr> <td class="h" > <a name="1670">1670</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> MRS server versions, but sometimes you have to tell what version you </td> </tr> <tr> <td class="h" > <a name="1671">1671</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> are planning to connect to. </td> </tr> <tr> <td class="h" > <a name="1672">1672</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1673">1673</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =head3 new parameter C<mrs_version> </td> </tr> <tr> <td class="h" > <a name="1674">1674</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1675">1675</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> By default, the C<MRS::Client> assumes that it connects to an MRS </td> </tr> <tr> <td class="h" > <a name="1676">1676</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> server version 6 (or higher). But for MRS servers version 5 you need </td> </tr> <tr> <td class="h" > <a name="1677">1677</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> to add a new argument B<mrs_version> to the client instance </td> </tr> <tr> <td class="h" > <a name="1678">1678</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> constructor with a value that differs from 6 (and it not zero or </td> </tr> <tr> <td class="h" > <a name="1679">1679</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> undef): </td> </tr> <tr> <td class="h" > <a name="1680">1680</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1681">1681</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> my $client = MRS::Client->new (mrs_version => 5, host => '...'); </td> </tr> <tr> <td class="h" > <a name="1682">1682</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1683">1683</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> You can also set the expected version by an environment variable </td> </tr> <tr> <td class="h" > <a name="1684">1684</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> C<MRS_VERSION>: </td> </tr> <tr> <td class="h" > <a name="1685">1685</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1686">1686</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> $ENV{MRS_VERSION} = 5; </td> </tr> <tr> <td class="h" > <a name="1687">1687</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> my $client = MRS::Client->new (host => '...'); </td> </tr> <tr> <td class="h" > <a name="1688">1688</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1689">1689</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> You can also check what version your client is talking to, by a new </td> </tr> <tr> <td class="h" > <a name="1690">1690</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> method B<is_v6> (mostly used rather internally): </td> </tr> <tr> <td class="h" > <a name="1691">1691</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1692">1692</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> $client->is_v6() # returns 1 or 0 </td> </tr> <tr> <td class="h" > <a name="1693">1693</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1694">1694</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> The command-line tool C<mrsclient> got an additional parameter B<-V>: </td> </tr> <tr> <td class="h" > <a name="1695">1695</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1696">1696</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> mrsclient -V5 -H... -l </td> </tr> <tr> <td class="h" > <a name="1697">1697</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1698">1698</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =head3 missing some result formats </td> </tr> <tr> <td class="h" > <a name="1699">1699</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1700">1700</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> The MRS 6 server does not support anymore B<HTML> and B<sequence> </td> </tr> <tr> <td class="h" > <a name="1701">1701</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> result formats. The C<sequence> format does not matter much because </td> </tr> <tr> <td class="h" > <a name="1702">1702</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> the C<fasta> format continues to be provided and it is easy to get the </td> </tr> <tr> <td class="h" > <a name="1703">1703</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> pure sequence from it. But the lack of the C<HTML> format is probably </td> </tr> <tr> <td class="h" > <a name="1704">1704</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> the most significant (downgrade) change. </td> </tr> <tr> <td class="h" > <a name="1705">1705</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1706">1706</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =head3 search algorithm not supported </td> </tr> <tr> <td class="h" > <a name="1707">1707</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1708">1708</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> The MRS 6 server does not accept anymore requests for different search </td> </tr> <tr> <td class="h" > <a name="1709">1709</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> algorithms; it uses always the B<Vector> algorithm. </td> </tr> <tr> <td class="h" > <a name="1710">1710</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1711">1711</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =head3 no ClustalW service </td> </tr> <tr> <td class="h" > <a name="1712">1712</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1713">1713</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> The MRS 6 server does not provide multiple sequence alignment </td> </tr> <tr> <td class="h" > <a name="1714">1714</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> service. All remarks about ClustalW in this document are, therefore, </td> </tr> <tr> <td class="h" > <a name="1715">1715</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> valid only for the MRS 5. </td> </tr> <tr> <td class="h" > <a name="1716">1716</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1717">1717</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =head3 aliases </td> </tr> <tr> <td class="h" > <a name="1718">1718</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1719">1719</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> The MRS 6 brings a new concept: I<aliases>. An alias is a set of </td> </tr> <tr> <td class="h" > <a name="1720">1720</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> databases, usually closely related. A typical example is an alias </td> </tr> <tr> <td class="h" > <a name="1721">1721</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> C<uniprot> that combines together two databases, the C<sprot> </td> </tr> <tr> <td class="h" > <a name="1722">1722</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> (SwissProt) and C<trembl> (TrEMBL). You can use an alias in all places </td> </tr> <tr> <td class="h" > <a name="1723">1723</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> where so far only database IDs were possible. </td> </tr> <tr> <td class="h" > <a name="1724">1724</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1725">1725</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> However, the list of databases returned by the "db()" method does not </td> </tr> <tr> <td class="h" > <a name="1726">1726</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> include the aliases. You need to ask individual databases for their </td> </tr> <tr> <td class="h" > <a name="1727">1727</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> aliases: </td> </tr> <tr> <td class="h" > <a name="1728">1728</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1729">1729</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> $client->db('sprot')->aliases(); </td> </tr> <tr> <td class="h" > <a name="1730">1730</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1731">1731</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =head1 MISSING FEATURES, CAVEATS, BUGS </td> </tr> <tr> <td class="h" > <a name="1732">1732</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1733">1733</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =over </td> </tr> <tr> <td class="h" > <a name="1734">1734</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1735">1735</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item * </td> </tr> <tr> <td class="h" > <a name="1736">1736</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1737">1737</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> The MRS distinguishes between so-called I<ranked queries> and </td> </tr> <tr> <td class="h" > <a name="1738">1738</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> I<boolean queries>, and it recognizes also I<boolean filters>. I </td> </tr> <tr> <td class="h" > <a name="1739">1739</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> probably need to learn more about their differences. That's why you </td> </tr> <tr> <td class="h" > <a name="1740">1740</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> may see some differences in query results shown by this module and the </td> </tr> <tr> <td class="h" > <a name="1741">1741</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> B<mrsweb> web application (an application distributed together with </td> </tr> <tr> <td class="h" > <a name="1742">1742</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> the implementation of the MRS servers). </td> </tr> <tr> <td class="h" > <a name="1743">1743</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1744">1744</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> The contents of the search field in the I<mrsweb> is first parsed in </td> </tr> <tr> <td class="h" > <a name="1745">1745</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> order to find out if it is a boolean expression, or not. Depending on </td> </tr> <tr> <td class="h" > <a name="1746">1746</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> the result it uses either a ranked or boolean query. It also splits </td> </tr> <tr> <td class="h" > <a name="1747">1747</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> the terms and combine them (by default) with the logical AND. For </td> </tr> <tr> <td class="h" > <a name="1748">1748</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> example, in I<mrsweb> if you type (using the F<uniprot>): </td> </tr> <tr> <td class="h" > <a name="1749">1749</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1750">1750</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> cone snail </td> </tr> <tr> <td class="h" > <a name="1751">1751</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1752">1752</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> you get 134 entries. You get the same number of hits by the </td> </tr> <tr> <td class="h" > <a name="1753">1753</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> C<MRS::Client> module when using an I<and> argument: </td> </tr> <tr> <td class="h" > <a name="1754">1754</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1755">1755</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> print $client->db('uniprot')->find ('and' => ['cone','snail'])->count; </td> </tr> <tr> <td class="h" > <a name="1756">1756</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> 134 </td> </tr> <tr> <td class="h" > <a name="1757">1757</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1758">1758</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> But you cannot just pass the whole expression as a query string (as </td> </tr> <tr> <td class="h" > <a name="1759">1759</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> you do in I<mrsweb>): </td> </tr> <tr> <td class="h" > <a name="1760">1760</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1761">1761</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> print $client->db('uniprot')->find ('cone snail')->count; </td> </tr> <tr> <td class="h" > <a name="1762">1762</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> 0 </td> </tr> <tr> <td class="h" > <a name="1763">1763</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1764">1764</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> You get zero entries because the C<MRS::Client> considers the above as </td> </tr> <tr> <td class="h" > <a name="1765">1765</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> one term. And if you add a boolean operator: </td> </tr> <tr> <td class="h" > <a name="1766">1766</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1767">1767</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> print $client->db('uniprot')->find ('cone AND snail')->count; </td> </tr> <tr> <td class="h" > <a name="1768">1768</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> 4609 </td> </tr> <tr> <td class="h" > <a name="1769">1769</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1770">1770</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> then the boolean query was used and, as explained by the MRS, the </td> </tr> <tr> <td class="h" > <a name="1771">1771</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> "query did not return an exact result, displaying the closest </td> </tr> <tr> <td class="h" > <a name="1772">1772</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> matches". But, fortunately, when you iterate over this result, you </td> </tr> <tr> <td class="h" > <a name="1773">1773</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> will get, correctly, just the 134 entries. </td> </tr> <tr> <td class="h" > <a name="1774">1774</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1775">1775</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =item * </td> </tr> <tr> <td class="h" > <a name="1776">1776</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1777">1777</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> The MRS servers provide few more operations that are not-yet covered </td> </tr> <tr> <td class="h" > <a name="1778">1778</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> by this module. It would be useful to discuss which of those are worth </td> </tr> <tr> <td class="h" > <a name="1779">1779</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> to implement. They are: </td> </tr> <tr> <td class="h" > <a name="1780">1780</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1781">1781</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> GetMetaData </td> </tr> <tr> <td class="h" > <a name="1782">1782</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> FindSimilar </td> </tr> <tr> <td class="h" > <a name="1783">1783</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> GetLinked </td> </tr> <tr> <td class="h" > <a name="1784">1784</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Cooccurrence </td> </tr> <tr> <td class="h" > <a name="1785">1785</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> SpellCheck </td> </tr> <tr> <td class="h" > <a name="1786">1786</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> SuggestSearchTerms </td> </tr> <tr> <td class="h" > <a name="1787">1787</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> CompareDocuments </td> </tr> <tr> <td class="h" > <a name="1788">1788</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> ClusterDocuments </td> </tr> <tr> <td class="h" > <a name="1789">1789</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1790">1790</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> There is also a potentially useful attribute I<links> in the </td> </tr> <tr> <td class="h" > <a name="1791">1791</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> databank's info which has not been yet explored by this module. </td> </tr> <tr> <td class="h" > <a name="1792">1792</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1793">1793</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =back </td> </tr> <tr> <td class="h" > <a name="1794">1794</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1795">1795</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =head1 ADDITIONAL FILES </td> </tr> <tr> <td class="h" > <a name="1796">1796</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1797">1797</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Almost all functionality of the C<MRS::Client> module is also </td> </tr> <tr> <td class="h" > <a name="1798">1798</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> available from a command-line controlled scripts F<mrsclient>, </td> </tr> <tr> <td class="h" > <a name="1799">1799</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> F<mrsblast> and F<mrsclustal>. Try , for example: </td> </tr> <tr> <td class="h" > <a name="1800">1800</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1801">1801</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> mrsclient -h </td> </tr> <tr> <td class="h" > <a name="1802">1802</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> mrsclient -C </td> </tr> <tr> <td class="h" > <a name="1803">1803</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> mrsclient -c -n insulin </td> </tr> <tr> <td class="h" > <a name="1804">1804</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> mrsclient -c -p -d enzyme -a 'endothelin tyrosine' </td> </tr> <tr> <td class="h" > <a name="1805">1805</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> mrsblast -h </td> </tr> <tr> <td class="h" > <a name="1806">1806</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> mrsclustal -h </td> </tr> <tr> <td class="h" > <a name="1807">1807</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1808">1808</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =head1 DEPENDENCIES </td> </tr> <tr> <td class="h" > <a name="1809">1809</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1810">1810</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> The C<MRS::Client> module uses the following modules: </td> </tr> <tr> <td class="h" > <a name="1811">1811</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1812">1812</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> XML::Compile::SOAP11 </td> </tr> <tr> <td class="h" > <a name="1813">1813</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> XML::Compile::WSDL11 </td> </tr> <tr> <td class="h" > <a name="1814">1814</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> XML::Compile::Transport::SOAPHTTP </td> </tr> <tr> <td class="h" > <a name="1815">1815</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> File::Basename </td> </tr> <tr> <td class="h" > <a name="1816">1816</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> File::Path </td> </tr> <tr> <td class="h" > <a name="1817">1817</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Math::BigInt </td> </tr> <tr> <td class="h" > <a name="1818">1818</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> FindBin </td> </tr> <tr> <td class="h" > <a name="1819">1819</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Getopt::Std </td> </tr> <tr> <td class="h" > <a name="1820">1820</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1821">1821</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =head1 BUGS </td> </tr> <tr> <td class="h" > <a name="1822">1822</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1823">1823</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Please report any bugs or feature requests to </td> </tr> <tr> <td class="h" > <a name="1824">1824</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> L<http://github.com/msenger/MRS-Client/issues>. </td> </tr> <tr> <td class="h" > <a name="1825">1825</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1826">1826</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =head1 ACKNOWLEDGMENTS </td> </tr> <tr> <td class="h" > <a name="1827">1827</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1828">1828</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> This client module would be useless without having an MRS server </td> </tr> <tr> <td class="h" > <a name="1829">1829</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> (e.g. at F<http://mrs.cmbi.ru.nl/m6/>). The MRS stands for </td> </tr> <tr> <td class="h" > <a name="1830">1830</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> B<Maarten's Retrieval System> and was developed (and is maintained) by </td> </tr> <tr> <td class="h" > <a name="1831">1831</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> I<Maarten Hekkelman> at the CMBI (F<http://www.cmbi.ru.nl/>), with the </td> </tr> <tr> <td class="h" > <a name="1832">1832</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> help and contributions from many others. </td> </tr> <tr> <td class="h" > <a name="1833">1833</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1834">1834</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> The MRS itself has also its own Perl module F<MRS.pm>, called plugin </td> </tr> <tr> <td class="h" > <a name="1835">1835</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> and distributed together with the MRS, that accesses MRS server(s) </td> </tr> <tr> <td class="h" > <a name="1836">1836</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> directly, without using the SOAP Web Services protocol. The plugin </td> </tr> <tr> <td class="h" > <a name="1837">1837</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> was helpful to find out what the server might expect. </td> </tr> <tr> <td class="h" > <a name="1838">1838</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1839">1839</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Additionally, the MRS distribution has few testing scripts that use </td> </tr> <tr> <td class="h" > <a name="1840">1840</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> SOAP protocol to access data in the same way as this C<MRS::Client> </td> </tr> <tr> <td class="h" > <a name="1841">1841</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> module does. Therefore, this module can be seen as an extension of </td> </tr> <tr> <td class="h" > <a name="1842">1842</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> these testing scripts into a slightly more comprehensive and perhaps </td> </tr> <tr> <td class="h" > <a name="1843">1843</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> more documented package. </td> </tr> <tr> <td class="h" > <a name="1844">1844</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1845">1845</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> The MRS server provides Blast results that are not in XML. In order to </td> </tr> <tr> <td class="h" > <a name="1846">1846</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> make an XML output, this module uses, hopefully, the same format and </td> </tr> <tr> <td class="h" > <a name="1847">1847</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> conversion as found in the MRS web application. </td> </tr> <tr> <td class="h" > <a name="1848">1848</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1849">1849</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =head1 AUTHOR </td> </tr> <tr> <td class="h" > <a name="1850">1850</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1851">1851</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> Martin Senger <martin.senger@gmail.com> </td> </tr> <tr> <td class="h" > <a name="1852">1852</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1853">1853</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =head1 COPYRIGHT AND LICENSE </td> </tr> <tr> <td class="h" > <a name="1854">1854</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1855">1855</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> This software is copyright (c) 2013 by Martin Senger, CBRC - KAUST (Computational Biology Research Center - King Abdullah University of Science and Technology) All Rights Reserved.. </td> </tr> <tr> <td class="h" > <a name="1856">1856</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1857">1857</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> This is free software; you can redistribute it and/or modify it under </td> </tr> <tr> <td class="h" > <a name="1858">1858</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> the same terms as the Perl 5 programming language system itself. </td> </tr> <tr> <td class="h" > <a name="1859">1859</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1860">1860</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> =cut </td> </tr> <tr> <td class="h" > <a name="1861">1861</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1862">1862</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s">   </td> </tr> <tr> <td class="h" > <a name="1863">1863</a> </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td >   </td> <td class="s"> __END__ </td> </tr> </table> </body> </html>