File Coverage

blib/lib/Bio/Tools/Run/Alignment/Blat.pm

Criterion	Covered	Total	%
statement	44	141	31.2
branch	9	64	14.0
condition	2	17	11.7
subroutine	14	31	45.1
pod	17	17	100.0
total	86	270	31.8

#
# Copyright Balamurugan Kumarasamy
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code

=head1 NAME

Bio::Tools::Run::Alignment::Blat

=head1 SYNOPSIS

 use Bio::Tools::Run::Alignment::Blat;
 my $factory = Bio::Tools::Run::Alignment::Blat->new(-db => $database);
 # $report is a Bio::SearchIO-compliant object
 my $report = $factory->run($seqobj);

=head1 DESCRIPTION

Wrapper module for Blat program. This newer version allows for all parameters to
be set by passing them as an option to new().

Key bits not implemented yet (TODO):

=over 3

=item * Implement all needed L methods

Missing are a few, including version().

=item * Re-implement using L

Would like to get this running under something less reliant on OS-dependent
changes within code.

=item * No .2bit or .nib conversions yet

These require callouts to faToNib or faTwoTwoBit, which may or may not be
installed on a user's machine.  We can possibly add functionality to
check for faToTwoBit/faToNib and other UCSC tools in the future.

=back

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists.  Your participation is much appreciated.

  [e-mail]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Support

Please direct usage questions or support issues to the mailing list:

I

rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.  Bug reports can be submitted via the
web:

  http://redmine.open-bio.org/projects/bioperl/

=head1 AUTHOR

 Chris Fields - cjfields at bioperl dot org

 Original author - Bala Email [e-mail]

=head1 APPENDIX

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _

=cut


package Bio::Tools::Run::Alignment::Blat;

use strict;
use warnings;
use base qw(Bio::Root::Root Bio::Tools::Run::WrapperBase);

use Bio::SeqIO;
use Bio::Root::Root;
use Bio::Factory::ApplicationFactoryI;
use Bio::SearchIO;
use Bio::Tools::Run::WrapperBase;

our ($PROGRAM, $PROGRAMDIR, $PROGRAMNAME);

our %BLAT_PARAMS = map {$_ => 1} qw(ooc t q tileSize stepSize oneOff
    minMatch minScore minIdentity maxGap makeOoc repmatch mask qMask repeats
    minRepeatsDivergence dots out maxIntron);

our %BLAT_SWITCHES = map {$_ => 1} qw(prot noHead trimT noTrimA trimHardA
                                    fastMap fine extendThroughN);

our %LOCAL_ATTRIBUTES = map {$_ => 1} qw(db DB qsegment hsegment searchio
                                    outfile_name quiet);

our %searchio_map = (
    'psl'     => 'psl',
    'pslx'    => 'psl', # I don't think there is support for this yet
    'axt'     => 'axt',
    'blast'   => 'blast',
    'sim4'    => 'sim4',
    'wublast' => 'blast',
    'blast8'  => 'blasttable',
    'blast9'  => 'blasttable'
);


=head2 new

 Title   : new
 Usage   : $blat->new( -db => '' )
 Function: Create a new Blat factory
 Returns : A new Bio::Tools::Run::Alignment::Blat object
 Args    : -db       : Mandatory parameter. See db()
           -qsegment : see qsegment()
           -tsegment : see tsegment()
           Also, Blat parameters and flags are accepted: -t, -q, -minIdentity,
              -minScore, -out, -trimT, ...
           See Blat's manual for details.

=cut

sub new {
    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);
    $self->io->_initialize_io();
    $self->set_parameters(@args);
    return $self;
}


=head2 program_name

 Title   : program_name
 Usage   : $factory->program_name()
 Function: Get the program name
 Returns : string
 Args    : None

=cut

sub program_name {
    return 'blat';
}


=head2 program_dir

 Title   : program_dir
 Usage   : $factory->program_dir(@params)
 Function: returns the program directory, obtained from ENV variable.
 Returns : string
 Args    :

=cut

sub program_dir {
    return Bio::Root::IO->catfile($ENV{BLATDIR}) if $ENV{BLATDIR};
}


=head2 run

 Title   : run()
 Usage   : $obj->run($query)
 Function: Run Blat.
 Returns : A Bio::SearchIO object that holds the results
 Args    : A Bio::PrimarySeqI object or a file of query sequences

=cut

sub run {
    my ($self, $query) = @_;
    if  (ref($query) ) {  # it is an object
        if (ref($query) =~ /GLOB/) {
            $self->throw("Cannot use filehandle as argument to run()");
        }
        $query = $self->_writeSeqFile($query);
    }
    return $self->_run($query);
}


=head2 align

 Title   : align
 Usage   : $obj->align($query)
 Function: Alias to run()

=cut

sub align {
    return shift->run(@_);
}


=head2 db

 Title   : db
 Usage   : $obj->db()
 Function: Get or set the file of database sequences (.fa , .nib or .2bit)
 Returns : Database filename
 Args    : Database filename

=cut

sub db {
    my $self = shift;
    return $self->{blat_db} = shift if @_;
    return $self->{blat_db};
}

# this is a kludge for tests (so one might expect this to be used elsewhere).
# None of the other parameters worked in the past, so not replacing them

*DB = \&db;


=head2 qsegment

 Title    : qsegment
 Usage    : $obj->qsegment('sequence_a:0-1000')
 Function : pass in a B string for the query sequence(s)
 Returns  : string
 Args     : string
 Note     : Requires the sequence(s) in question be 2bit or nib format
 Reminder : UCSC segment/regions coordinates are 0-based half-open (sequence
            begins at 0, but start isn't counted with length), whereas BioPerl
            coordinates are 1-based closed (sequence begins with 1, both start
            and end are counted in the length of the segment). For example, a
            segment that is 'sequence_a:0-1000' will have BioPerl coordinates of
            'sequence_a:1-1000', both with the same length (1000).

=cut

sub qsegment {
    my $self = shift;
    return $self->{blat_qsegment} = shift if @_;
    return $self->{blat_qsegment};
}


=head2 tsegment

 Title    : tsegment
 Usage    : $obj->tsegment('sequence_a:0-1000')
 Function : pass in a B string for the target sequence(s)
 Returns  : string
 Args     : string
 Note     : Requires the sequence(s) in question be 2bit or nib format
 Reminder : UCSC segment/regions coordinates are 0-based half-open (sequence
            begins at 0, but start isn't counted with length), whereas BioPerl
            coordinates are 1-based closed (sequence begins with 1, both start
            and end are counted in the length of the segment). For example, a
            segment that is 'sequence_a:0-1000' will have BioPerl coordinates of
            'sequence_a:1-1000', both with the same length (1000).

=cut

sub tsegment {
    my $self = shift;
    return $self->{blat_tsegment} = shift if @_;
    return $self->{blat_tsegment};
}


=head2 outfile_name

 Title    : outfile_name
 Usage    : $obj->outfile_name('out.blat')
 Function : Get or set the name for the BLAT output file
 Returns  : string
 Args     : string

=cut

# override this, otherwise one gets a default of 'mlc'
sub outfile_name {
    my $self = shift;
    return $self->{blat_outfile} = shift if @_;
    return $self->{blat_outfile};
}


=head2 searchio

 Title    : searchio
 Usage    : $obj->searchio{-writer => $writer}
 Function : Pass in additional parameters to the returned Bio::SearchIO parser
 Returns  : Hash reference with Bio::SearchIO parameters
 Args     : Hash reference
 Note     : Currently, this implementation overrides any passed -format
            parameter based on whether the output is changed ('out').  This
            may change if requested, but we can't see the utility of doing so,
            as requesting mismatched output/parser combinations is just a recipe
            for disaster

=cut

sub searchio {
    my ($self, $params) = @_;
    if ($params && ref $params eq 'HASH') {
        delete $params->{-format};
        $self->{blat_searchio} = $params;
    }
    return $self->{blat_searchio} || {};
}


=head1 Bio::ParameterBaseI-specific methods

These methods are part of the Bio::ParameterBaseI interface

=head2 set_parameters

 Title   : set_parameters
 Usage   : $pobj->set_parameters(%params);
 Function: sets the parameters listed in the hash or array
 Returns : None
 Args    : [optional] hash or array of parameter/values.  These can optionally
           be hash or array references
 Note    : This only sets parameters; to set methods use the method name

=cut

sub set_parameters {
    my $self = shift;
    # circumvent any issues arising from passing in refs
    my %args = (ref($_[0]) eq 'HASH')  ? %{$_[0]} :
               (ref($_[0]) eq 'ARRAY') ? @{$_[0]} :
               @_;
    # set the parameters passed in, but only ones supported for the program
    %args = map { my $a = $_;
              $a =~ s{^-}{};
              $a => $args{$_};
                 } sort keys %args;

    while (my ($key, $val) = each %args) {
        if (exists $BLAT_PARAMS{$key}) {
            $self->{parameters}->{$key} = $val;
        } elsif (exists $BLAT_SWITCHES{$key}) {
            $self->{parameters}->{$key} = $BLAT_SWITCHES{$key} ? 1 : 0;
        } elsif ($LOCAL_ATTRIBUTES{$key} && $self->can($key)) {
            $self->$key($val);
        }
    }
}


=head2 reset_parameters

 Title   : reset_parameters
 Usage   : resets values
 Function: resets parameters to either undef or value in passed hash
 Returns : none
 Args    : [optional] hash of parameter-value pairs

=cut

sub reset_parameters {
    my $self = shift;
    delete $self->{parameters};
    if (@_) {
        $self->set_parameters(@_);
    }
}


=head2 validate_parameters

 Title   : validate_parameters
 Usage   : $pobj->validate_parameters(1);
 Function: sets a flag indicating whether to validate parameters via
           set_parameters() or reset_parameters()
 Returns : Bool
 Args    : [optional] value evaluating to True/False
 Note    : NYI

=cut

sub validate_parameters { 0 }


=head2 parameters_changed

 Title   : parameters_changed
 Usage   : if ($pobj->parameters_changed) {...}
 Function: Returns boolean true (1) if parameters have changed
 Returns : Boolean (0 or 1)
 Args    : None
 Note    : This module does not run state checks, so this always returns True

=cut

sub parameters_changed { 1 }


=head2 available_parameters

 Title   : available_parameters
 Usage   : @params = $pobj->available_parameters()
 Function: Returns a list of the available parameters
 Returns : Array of parameters
 Args    : [optional] name of executable being used; defaults to returning all
           available parameters

=cut

sub available_parameters {
    my ($self, $exec) = @_;
    my @params = (sort keys %BLAT_PARAMS, sort keys %BLAT_SWITCHES);
    return @params;
}


=head2 get_parameters

 Title   : get_parameters
 Usage   : %params = $pobj->get_parameters;
 Function: Returns list of set key-value pairs, parameter => value
 Returns : List of key-value pairs
 Args    : none

=cut

sub get_parameters {
    my ($self, $option) = @_;
    $option ||= ''; # no option
    my %params;
    if (exists $self->{parameters}) {
        %params = map {$_ => $self->{parameters}->{$_}} sort keys %{$self->{parameters}};
    } else {
        %params = ();
    }
    return %params;
}


=head1 to_* methods

All to_* methods are implementation-specific

=head2 to_exe_string

 Title   : to_exe_string
 Usage   : $string = $pobj->to_exe_string;
 Function: Returns string (command line string in this case)
 Returns : String
 Args    :

=cut

sub to_exe_string {
    my ($self, @passed) = @_;
    my ($seq) = $self->_rearrange([qw(SEQ_FILE)], @passed);
    $self->throw("Must provide a seq_file") unless defined $seq;
    my %params = $self->get_parameters();

    my ($exe, $db, $qseg, $tseg) = ($self->executable,
                                   $self->db,
                                   $self->qsegment,
                                   $self->tsegment);

    $self->throw("Executable not found") unless defined($exe);

    if ($tseg) {
        $db .= ":$tseg";
    }

    if ($qseg) {
        $seq .= ":$qseg";
    }

    my @params;

    for my $p (sort keys %BLAT_SWITCHES) {
        if (exists $params{$p}) {
            push @params, "-$p"
        }
    }

    for my $p (sort keys %BLAT_PARAMS) {
        if (exists $params{$p}) {
            push @params, "-$p=$params{$p}"
        }
    }

    # this only passes in the first seq file (no globs are allow AFAIK)

    push @params, ($db, $seq);

    # quiet! Unfortunately, it is NYI

    my $string = "$exe ".join(' ',@params);

    return $string;
}


#=head2 _input
#
# Title   : _input
# Usage   : obj->_input($seqFile)
# Function: Internal (not to be used directly)
# Returns :
# Args    :
#
#=cut

sub _input() {
    my ($self,$infile1) = @_;
    if (defined $infile1) {
        $self->{'input'} = $infile1;
    }
    return $self->{'input'};
}


#=head2 _database
#
# Title   : _database
# Usage   : obj->_database($seqFile)
# Function: Internal (not to be used directly)
# Returns :
# Args    :
#
#=cut

sub _database() {
    my ($self,$infile1) = @_;
    $self->{'db'} = $infile1 if(defined $infile1);
    return $self->{'db'};
}


#=head2 _run
#
# Title   : _run
# Usage   : $obj->_run()
# Function: Internal (not to be used directly)
# Returns : A Bio::SearchIO object that contains the results
# Args    : File of sequences
#
#=cut

sub _run {
    my ($self, $seq_file) = @_;
    my $str = $self->to_exe_string(-seq_file => $seq_file);

    my $out = $self->outfile_name || $self->_tempfile;

    $str .= " $out".$self->_quiet;
    $self->debug($str."\n") if( $self->verbose > 0 );

    my %params = $self->get_parameters;

    my $status = system($str);
    $self->throw( "Blat call ($str) crashed: $? \n") unless $status==0;

    my $format = exists($params{out}) ?
                $searchio_map{$params{out}} : 'psl';

    my @io = ref ($out) !~ /GLOB/ ? (-file    => $out,) : (-fh    => $out,);
    my $blat_obj = Bio::SearchIO->new(%{$self->searchio},
                                    @io,
                                    -query_type => $params{prot} ? 'protein' :
                                                    $params{q} || 'dna',
                                    -hit_type   => $params{prot} ? 'protein' :
                                                    $params{t} || 'dna',
                                    -format => $format);
    return $blat_obj;
}


#=head2 _writeSeqFile
#
# Title   : _writeSeqFile
# Usage   : obj->_writeSeqFile($seq)
# Function: Internal (not to be used directly)
# Returns :
# Args    :
#
#=cut

sub _writeSeqFile {
    my ($self,$seq) = @_;
    my ($tfh,$inputfile) = $self->io->tempfile(-dir=>$Bio::Root::IO::TEMPDIR);
    my $in  = Bio::SeqIO->new(-fh => $tfh , '-format' => 'fasta');
    $in->write_seq($seq);
    $in->close();
    return $inputfile;
}


sub _tempfile {
    my $self = shift;
    my ($tfh,$outfile) = $self->io->tempfile(-dir=>$Bio::Root::IO::TEMPDIR);
    # this is because we only want a unique filename
    close($tfh);
    return $outfile;
}


sub _quiet {
    my $self = shift;
    my $q = '';
    # BLAT output goes to a file, all other output is STDOUT
    if ($self->quiet) {
        $q =  $^O =~ /Win/i ? ' 2>&1 NUL' : ' > /dev/null 2>&1';
    }
    return $q;
}

1;