[Bioperl-l] [Bioperl-guts-l] [14510] bioperl-live/trunk/Bio/SeqIO/swiss.pm: GN line output now follows the new format.

Heikki Lehvaslaiho heikki at sanbi.ac.za
Mon Feb 18 03:12:11 EST 2008


Thanks for pointing this out to me. Looks like I've solved the first level:

"Problem #1 is to have all the value tokens
available from the created object, regardless of their tags."

Anybody want to go on to the next level and code in the complete 
representation of the GN line?

	-Heikki


On Sunday 17 February 2008 16:07:20 Chris Fields wrote:
> Heikki,
>
> See bug 1825:
>
> http://bugzilla.open-bio.org/show_bug.cgi?id=1825
>
> Hilmar's final comments about restructuring
> Bio::Annotation::StructuredValue using Data::Stag should work.
>
> chris
>
> On Feb 17, 2008, at 4:00 AM, Heikki Lehvaslaiho wrote:
> > Revision: 14510
> > Author:   heikki
> > Date:     2008-02-17 05:00:50 -0500 (Sun, 17 Feb 2008)
> >
> > Log Message:
> > -----------
> > GN line output now follows the new format. BioPerl would need new
> > objects to store all infomation so for now only the official name
> > (Name=) and synonym categories are kept. ORFNames and
> > OrderedLocusNames are treated as synonyms.
> >
> > Modified Paths:
> > --------------
> >    bioperl-live/trunk/Bio/SeqIO/swiss.pm
> >
> > Modified: bioperl-live/trunk/Bio/SeqIO/swiss.pm
> > ===================================================================
> > --- bioperl-live/trunk/Bio/SeqIO/swiss.pm	2008-02-17 09:48:07 UTC
> > (rev 14509)
> > +++ bioperl-live/trunk/Bio/SeqIO/swiss.pm	2008-02-17 10:00:50 UTC
> > (rev 14510)
> > @@ -494,16 +494,13 @@
> >     #Definition lines
> >     $self->_write_line_swissprot_regex("DE   ","DE   ",$seq-
> >
> > >desc(),"\\s\+\|\$",$LINE_LENGTH);
> >
> > -    #Gene name
> > -    if ((my @genes = $seq->annotation-
> >
> > >get_Annotations('gene_name') ) ) {
> >
> > -        $self->_print("GN   ",
> > -              join(' OR ',
> > -                   map {
> > -                   $_->isa("Bio::Annotation::StructuredValue") ?
> > -                       $_->value(-joins => [" AND ", " OR "]) :
> > -                       $_->value();
> > -                   } @genes),
> > -              ".\n");
> > +    #Gene name; print out new format but only two categories: Name
> > and Synonyms
> > +    if ( my @genes = $seq->annotation-
> >
> > >get_Annotations('gene_name') ) {
> >
> > +        my @gene_names = map { $_->get_all_values} @genes;
> > +        my $gn_string = 'Name='. shift(@gene_names). ';';
> > +        $gn_string .= ' Synonyms='. join(', ', @gene_names). ";" if
> > scalar @gene_names;
> > +        $self->_write_line_swissprot_regex("GN   ","GN   ",
> > $gn_string,"\\s\+\|\$",$LINE_LENGTH);
> > +
> >     }
> >
> >     # Organism lines
> > @@ -1267,7 +1264,6 @@
> >    }
> >
> >    my $subl = $length - (length $pre1) -1 ;
> > -   my @lines;
> >
> >    my $first_line = 1;
> >    while($line =~ m/(.{1,$subl})($regex)/g) {
> >
> >
> > _______________________________________________
> > Bioperl-guts-l mailing list
> > Bioperl-guts-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-guts-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



-- 
______ _/      _/_____________________________________________________
      _/      _/
     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
    _/_/_/_/_/  Senior Scientist    skype: heikki_lehvaslaiho
   _/  _/  _/  SANBI, South African National Bioinformatics Institute
  _/  _/  _/  University of Western Cape, South Africa
     _/      Phone: +27 21 959 2096   FAX: +27 21 959 2512
___ _/_/_/_/_/________________________________________________________


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