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Viewing changes to Bio/SeqFeature/Tools/Unflattener.pm

  • Committer: Package Import Robot
  • Author(s): Charles Plessy
  • Date: 2013-09-22 13:39:48 UTC
  • mfrom: (3.1.11 sid)
  • Revision ID: package-import@ubuntu.com-20130922133948-c6z62zegjyp7ztou
Tags: 1.6.922-1
http://bugs.debian.org/722910
* New upstream release.
* Replaces and Breaks grinder (<< 0.5.3-3~) because of overlaping contents.
  Closes: #722910
* Stop Replacing and Breaking bioperl ( << 1.6.9 ): not needed anymore. 

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Bio/SeqFeature/Tools/Unflattener.pm
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   # modify the original Seq object - the top seqfeatures are now
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   # the top features from each group
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   $seq->remove_SeqFeatures;
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   $seq->add_SeqFeature(@top_sfs);
 
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   $seq->add_SeqFeature($_) foreach @top_sfs;
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   # --------- FINISHED UNFLATTENING -------------
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           }
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       }
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       # SPECIAL CASE FOR /ribosomal_slippage
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       # See: http://www.ncbi.nlm.nih.gov/collab/FT/
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       if (!$inside && $sf->has_tag('ribosomal_slippage')) {
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           if ($self->verbose > 0) {
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               printf STDERR "    Checking for ribosomal_slippage\n";
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           }
 
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           # TODO: rewrite this to match introns;
 
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           #  each slippage will be a "fake" small CDS exon
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           my @transcript_splice_sites = @container_coords;
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           my @cds_splice_sites = @coords;
 
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           ##printf STDERR "xxTR SSs: @transcript_splice_sites :: %s\n", $_->get_tag_values('product');
 
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           ##printf STDERR "xxCD SSs: @cds_splice_sites :: %s\n\n", $sf->get_tag_values('product');
 
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           # find the the first splice site within the CDS
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           while (scalar(@transcript_splice_sites) &&
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                  $transcript_splice_sites[0] < $cds_splice_sites[0]) {
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               shift @transcript_splice_sites;
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           }
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           if ($transcript_splice_sites[0] == $cds_splice_sites[0]) {
 
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           ##print STDERR "TR SSs: @transcript_splice_sites\n";
 
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           ##print STDERR "CD SSs: @cds_splice_sites\n\n";
 
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           if (!(scalar(@transcript_splice_sites)) ||
 
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                 $transcript_splice_sites[0] == $cds_splice_sites[0]) {
 
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               # we will now try and align all splice remaining sites in the transcript and CDS;
 
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               # any splice site that can't be aligned is assumed to be a ribosomal slippage
 
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               my @slips = ();
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               my $in_exon = 1;
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               $inside = 1;   # innocent until proven guilty..
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               while (@cds_splice_sites) {
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                   if (!@transcript_splice_sites) {
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                       $inside = 0; # guilty!
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                       last;
 
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                       # ribosomal slippage is after the last transcript splice site
 
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                       # Example: (NC_00007, isoform 3 of PEG10)
 
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                       #     mRNA            join(85682..85903,92646..99007)
 
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                       #     mRNA            join(85682..85903,92646..99007)
 
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                       #     CDS             join(85899..85903,92646..93825,93825..94994)
 
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                       # OR: None of the splice sites align;
 
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                       #  may be a single CDS exon with one slippage inside it.
 
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                       # Example: (NC_00007, isoform 4 of PEG10)
 
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                       #     mRNA            join(85637..85892,92646..99007)
 
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                       #     CDS             join(92767..93825,93825..94994)
 
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                       # Yes, this code is repeated below...
 
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                       my $p1 = shift @cds_splice_sites;
 
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                       my $p2 = shift @cds_splice_sites;
 
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                       if ($self->verbose > 0) {
 
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                           printf STDERR "    Found the ribosomal_slippage: $p1..$p2\n";
 
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                       }
 
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                       push(@slips, ($p2-$p1)-1);
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                   }
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                   if ($cds_splice_sites[0] == $transcript_splice_sites[0]) {
 
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                   elsif ($cds_splice_sites[0] == $transcript_splice_sites[0]) {
 
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                       # splice sites align: this is not the slippage
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                       shift @cds_splice_sites;
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                       shift @transcript_splice_sites;
 
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                       ##print STDERR "MATCH\n";
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                   }
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                   else {
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                       # mismatch
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                           # ---TTTTTTTTTT----
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                           # ---CCCC--CCCC----
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                           #       ^
 
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                           my $p1 = shift @cds_splice_sites;
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                           my $p2 = shift @cds_splice_sites;
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                           if ($self->verbose > 0) {
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                       else {
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                           # not a potential ribosomal slippage
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                           $inside = 0; # guilty!
 
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                           ##print STDERR "FAIL\n";
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                           last;
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                       }
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                   }