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Viewing changes to Bio/SeqIO/fasta.pm

  • Committer: Bazaar Package Importer
  • Author(s): Charles Plessy
  • Date: 2009-03-10 07:19:11 UTC
  • mfrom: (1.2.3 upstream)
  • Revision ID: james.westby@ubuntu.com-20090310071911-fukqzw54pyb1f0bd
Tags: 1.6.0-2
https://launchpad.net/bugs/324001
* Removed patch system (not used):
  - removed instuctions in debian/rules;
  - removed quilt from Build-Depends in debian/control.
* Re-enabled tests:
  - uncommented test command in debian/rules;
  - uncommented previously missing build-dependencies in debian/control.
  - Re-enabled tests and uncommented build-dependencies accordingly.
* Removed libmodule-build-perl and libtest-harness-perl from
  Build-Depends-Indep (provided by perl-modules).
* Better cleaning of empty directories using find -type d -empty -delete
  instead of rmdir in debian/rules (LP: #324001).

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Bio/SeqIO/fasta.pm
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# $Id: fasta.pm,v 1.58.4.1 2006/10/02 23:10:29 sendu Exp $
 
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# $Id: fasta.pm 14669 2008-04-22 21:03:23Z cjfields $
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# BioPerl module for Bio::SeqIO::fasta
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#
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# Cared for by Ewan Birney <birney@ebi.ac.uk>
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                $self->throw("Did not provide a valid Bio::PrimarySeqI object") 
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                  unless defined $seq && ref($seq) && $seq->isa('Bio::PrimarySeqI');
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                my $str = $seq->seq;
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                my $top;
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                # Allow for different ids 
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                        $desc =~ s/\n//g;
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                        $top .= " $desc";
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                }
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                if(defined $str && length($str) > 0) {
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                        $str =~ s/(.{1,$width})/$1\n/g;
 
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                if( $seq->isa('Bio::Seq::LargeSeqI') ) {
 
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                  $self->_print(">$top\n");
 
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                  # for large seqs, don't call seq(), it defeats the
 
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                  # purpose of the largeseq functionality.  instead get
 
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                  # chunks of the seq, $width at a time
 
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                  my $buff_max = 2000;
 
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                  my $buff_size = int($buff_max/$width)*$width; #< buffer is even multiple of widths
 
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                  my $seq_length = $seq->length;
 
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                  my $num_chunks = int($seq_length/$buff_size+1);
 
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                  for( my $c = 0; $c < $num_chunks; $c++ ) {
 
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                    my $buff_end = $buff_size*($c+1);
 
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                    $buff_end = $seq_length if $buff_end > $seq_length;
 
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                    my $buff = $seq->subseq($buff_size*$c+1,$buff_end);
 
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                    if($buff) {
 
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                      $buff =~ s/(.{1,$width})/$1\n/g;
 
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                      $self->_print($buff);
 
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                    } else {
 
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                      $self->_print("\n");
 
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                    }
 
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                  }
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                } else {
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                        $str = "\n";
 
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                  my $str = $seq->seq;
 
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                  if(defined $str && length($str) > 0) {
 
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                    $str =~ s/(.{1,$width})/$1\n/g;
 
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                  } else {
 
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                    $str = "\n";
 
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                  }
 
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                  $self->_print (">",$top,"\n",$str) or return;
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                }
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                $self->_print (">",$top,"\n",$str) or return;
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   }
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   $self->flush if $self->_flush_on_write && defined $self->_fh;