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

Chris Fields cjfields at uiuc.edu
Sun Feb 17 09:07:20 EST 2008


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) {
>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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