[Bioperl-l] Re: [Bioperl-guts-l] bioperl-live/Bio/FeatureIO gff.pm, 1.16, 1.17

[Allen Day]

there should be a next_sequence method.  i wrote this into
Bio::Tools::GFF, we should pretty much be able to just copy/paste it over.

-allen


On Tue, 16 Nov 2004, Scott Cain wrote:

> Update of /home/repository/bioperl/bioperl-live/Bio/FeatureIO
> In directory pub.open-bio.org:/tmp/cvs-serv5204
> 
> Modified Files:
> 	gff.pm 
> Log Message:
> added stuff to support fasta and target processing.  The quesion remains what to 
> do with this data once you have it--particularly the fasta data.  Should there be
> (or is there) a next_sequence() method?
> 
> 
> Index: gff.pm
> ===================================================================
> RCS file: /home/repository/bioperl/bioperl-live/Bio/FeatureIO/gff.pm,v
> retrieving revision 1.16
> retrieving revision 1.17
> diff -C2 -d -r1.16 -r1.17
> *** gff.pm	16 Nov 2004 16:22:53 -0000	1.16
> --- gff.pm	16 Nov 2004 19:35:09 -0000	1.17
> ***************
> *** 211,215 ****
>     return undef unless $gff_string;
>   
> !   if($gff_string =~ /^##/){
>       $self->_handle_directive($gff_string);
>       return $self->next_feature();
> --- 211,215 ----
>     return undef unless $gff_string;
>   
> !   if($gff_string =~ /^##/ or $gff_string =~ /^>/){
>       $self->_handle_directive($gff_string);
>       return $self->next_feature();
> ***************
> *** 248,255 ****
>     }
>   
> !   elsif($directive eq 'FASTA'){
>       $self->warn("'##$directive' directive handling not yet implemented");
> !     while($self->_readline()){
> !       #suck up the rest of the file
>       }
>     }
> --- 248,266 ----
>     }
>   
> !   elsif($directive eq 'FASTA' or $directive =~ /^>(.+)/){
> !     my $fasta_directive_id = $1 if $1;
>       $self->warn("'##$directive' directive handling not yet implemented");
> !     local $/ = '>';
> !     while(my $read = $self->_readline()){
> !        chomp $read;
> !        my $fasta_id;
> !        my @seqarray = split /\n/, $read;
> !        if ($fasta_directive_id) {
> !          $fasta_id = $fasta_directive_id;
> !          $fasta_directive_id = '';
> !        } else {
> !          $fasta_id = shift @seqarray;
> !        }
> !        my $seq = join '', @seqarray;
>       }
>     }
> ***************
> *** 357,363 ****
>         ); 
>   
> !       if ($strand eq '+') {
>           $strand = 1;
> !       } elsif ($strand eq '-') {
>           $strand = -1;
>         }
> --- 368,374 ----
>         ); 
>   
> !       if ($strand && $strand eq '+') {
>           $strand = 1;
> !       } elsif ($strand && $strand eq '-') {
>           $strand = -1;
>         }
> 
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