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# BioPerl module for Bio::SeqFeature::Gene::Exon |
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# |
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# Please direct questions and support issues to |
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# |
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# Cared for by Hilmar Lapp |
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# Copyright Hilmar Lapp |
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# |
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# You may distribute this module under the same terms as perl itself |
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# POD documentation - main docs before the code |
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=head1 NAME |
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Bio::SeqFeature::Gene::Exon - a feature representing an exon |
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=head1 SYNOPSIS |
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# obtain an exon instance $exon somehow |
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print "exon from ", $exon->start(), " to ", $exon->end(), |
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" on seq ", $exon->seq_id(), ", strand ", $exon->strand(), |
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", encodes the peptide sequence ", |
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$exon->cds()->translate()->seq(), "\n"; |
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=head1 DESCRIPTION |
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This module implements a feature representing an exon by implementing |
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the Bio::SeqFeature::Gene::ExonI interface. By default an Exon is |
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coding. Supply -is_coding =E 0 to the constructor or call |
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$exon-Eis_coding(0) otherwise. |
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Apart from that, this class also implements Bio::SeqFeatureI by |
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inheriting off Bio::SeqFeature::Generic. |
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=head1 FEEDBACK |
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=head2 Mailing Lists |
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User feedback is an integral part of the evolution of this |
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and other Bioperl modules. Send your comments and suggestions preferably |
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to one of the Bioperl mailing lists. |
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Your participation is much appreciated. |
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bioperl-l@bioperl.org - General discussion |
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http://bioperl.org/wiki/Mailing_lists - About the mailing lists |
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=head2 Support |
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Please direct usage questions or support issues to the mailing list: |
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I |
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rather than to the module maintainer directly. Many experienced and |
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reponsive experts will be able look at the problem and quickly |
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address it. Please include a thorough description of the problem |
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with code and data examples if at all possible. |
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=head2 Reporting Bugs |
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Report bugs to the Bioperl bug tracking system to help us keep track |
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the bugs and their resolution. Bug reports can be submitted via the |
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web: |
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https://github.com/bioperl/bioperl-live/issues |
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=head1 AUTHOR - Hilmar Lapp |
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Email hlapp@gmx.net |
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=head1 APPENDIX |
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The rest of the documentation details each of the object methods. |
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Internal methods are usually preceded with a _ |
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=cut |
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# Let the code begin... |
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package Bio::SeqFeature::Gene::Exon; |
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use strict; |
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use base qw(Bio::SeqFeature::Generic Bio::SeqFeature::Gene::ExonI); |
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# |
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# A list of allowed exon types. See primary_tag(). |
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# |
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my @valid_exon_types = ('initial', 'internal', 'terminal'); |
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sub new { |
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my ($caller, @args) = @_; |
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my $self = $caller->SUPER::new(@args); |
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my ($is_coding) = |
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$self->_rearrange([qw(IS_CODING)],@args); |
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$self->primary_tag('exon') unless $self->primary_tag(); |
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$self->is_coding(defined($is_coding) ? $is_coding : 1); |
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$self->strand(0) if(! defined($self->strand())); |
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return $self; |
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} |
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=head2 is_coding |
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Title : is_coding |
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Usage : if($exon->is_coding()) { |
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# do something |
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} |
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if($is_utr) { |
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$exon->is_coding(0); |
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} |
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Function: Get/set whether or not the exon codes for amino acid. |
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Returns : TRUE if the object represents a feature translated into protein, |
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and FALSE otherwise. |
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Args : A boolean value on set. |
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=cut |
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sub is_coding { |
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my ($self,$val) = @_; |
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if(defined($val)) { |
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$self->{'_iscoding'} = $val; |
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} |
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return $self->{'_iscoding'}; |
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} |
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=head2 primary_tag |
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Title : primary_tag |
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Usage : $tag = $feat->primary_tag() |
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$feat->primary_tag('exon') |
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Function: Get/set the primary tag for the exon feature. |
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This method is overridden here in order to allow only for |
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tag values following a certain convention. For consistency reasons, |
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the tag value must either contain the string 'exon' or the string |
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'utr' (both case-insensitive). In the case of 'exon', a string |
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describing the type of exon may be appended or prefixed. Presently, |
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the following types are allowed: initial, internal, and terminal |
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(all case-insensitive). |
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If the supplied tag value matches 'utr' (case-insensitive), |
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is_coding() will automatically be set to FALSE, and to TRUE |
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otherwise. |
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Returns : A string. |
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Args : A string on set. |
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=cut |
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# sub primary_tag { |
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# my ($self,$value) = @_; |
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# if(defined($value)) { |
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# if((lc($value) =~ /utr/i) || (lc($value) eq "exon") || |
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# ((lc($value) =~ /exon/i) && |
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# (grep { $value =~ /$_/i; } @valid_exon_types))) { |
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# $self->is_coding($value =~ /utr/i ? 0 : 1); |
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# } else { |
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# $self->throw("primary tag $value is invalid for object of class ". |
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# ref($self)); |
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# } |
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# } |
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# return $self->SUPER::primary_tag($value); |
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# } |
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=head2 location |
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Title : location |
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Usage : my $location = $exon->location() |
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Function: Returns a location object suitable for identifying the location |
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of the exon on the sequence or parent feature. |
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This method is overridden here to restrict allowed location types |
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to non-compound locations. |
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Returns : Bio::LocationI object |
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Args : none |
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=cut |
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sub location { |
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5665
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5665
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my ($self,$value) = @_; |
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192
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5665
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7833
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if(defined($value) && $value->isa('Bio::Location::SplitLocationI')) { |
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$self->throw("split or compound location is not allowed ". |
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"for an object of type " . ref($self)); |
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} |
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8012
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return $self->SUPER::location($value); |
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} |
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=head2 cds |
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201
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Title : cds() |
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Usage : $cds = $exon->cds(); |
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Function: Get the coding sequence of the exon as a sequence object. |
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The sequence of the returned object is prefixed by Ns (lower case) |
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if the frame of the exon is defined and different from zero. The |
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result is that the first base starts a codon (frame 0). |
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209
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This implementation returns undef if the particular exon is |
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not translated to protein, i.e., is_coding() returns FALSE. Undef |
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will also be returned if no sequence is attached to this exon |
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feature. |
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214
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Returns : A Bio::PrimarySeqI implementing object. |
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Args : |
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217
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218
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=cut |
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220
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sub cds { |
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1
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1
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1
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2
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my ($self) = @_; |
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223
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# UTR is not translated |
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1
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50
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3
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return if(! $self->is_coding()); |
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226
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1
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116
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my $seq = $self->seq(); |
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1
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50
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33
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5
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if(defined($seq) && defined($self->frame()) && ($self->frame() != 0)) { |
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33
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228
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1
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3
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my $prefix = "n" x $self->frame(); |
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1
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79
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$seq->seq($prefix . $seq->seq()); |
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} |
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1
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3
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return $seq; |
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|
} |
233
|
|
|
|
|
|
|
|
234
|
|
|
|
|
|
|
1; |