[Bioperl-guts-l] bioperl-live/Bio/AlignIO stockholm.pm,1.28,1.29

Christopher John Fields cjfields at dev.open-bio.org
Tue Mar 20 12:31:10 EDT 2007


Update of /home/repository/bioperl/bioperl-live/Bio/AlignIO
In directory dev.open-bio.org:/tmp/cvs-serv12785

Modified Files:
	stockholm.pm 
Log Message:
Changed throw() due to verbose output from Infernal programs choking the stockholm parser

Index: stockholm.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/AlignIO/stockholm.pm,v
retrieving revision 1.28
retrieving revision 1.29
diff -C2 -d -r1.28 -r1.29
*** stockholm.pm	27 Nov 2006 15:36:10 -0000	1.28
--- stockholm.pm	20 Mar 2007 16:31:08 -0000	1.29
***************
*** 268,272 ****
      my $line;
  
!     my ($start, $end, $id, $name, $seqname, $seq, $count, $tag, $data);
      my $seen_rc;
      my ($refct, $bct, $lnkct) = (0,0,0);
--- 268,273 ----
      my $line;
  
!     my ($id, $name, $seqname, $seq, $count, $tag, $data);
!     my $start = my $end = 0;
      my $seen_rc;
      my ($refct, $bct, $lnkct) = (0,0,0);
***************
*** 281,289 ****
      my $aln =  Bio::SimpleAlign->new(-source => 'stockholm');
      while( defined($line = $self->_readline) ) {
!         next unless $line =~ /\w+/;
          if ($line =~ /^#\s*STOCKHOLM\s+/) {
              last;
          } else {
!             $self->throw("Not Stockholm format: Expecting \"# STOCKHOLM\"; Found \"$_\"");
          }
      }
--- 282,292 ----
      my $aln =  Bio::SimpleAlign->new(-source => 'stockholm');
      while( defined($line = $self->_readline) ) {
!         next if $line =~ /^\s*$/;
          if ($line =~ /^#\s*STOCKHOLM\s+/) {
              last;
          } else {
!             $line = $self->_readline;
!             # commented this out since some programs have headers with extra output
!             # $self->throw("Not Stockholm format: Expecting \"# STOCKHOLM\"; Found \"$line\"");
          }
      }
***************
*** 463,468 ****
      }
  
-     #$self->debug(Dumper($coll));
- 
      # add annotations
      $aln->annotation($coll); 
--- 466,469 ----



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