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

[Chris Mungall]

Is a group defined as a set of connected features?

Is the group required to end with a ### directive? This could be checked
for automatically by testing whether each feature is connected to the
current feature graph. Or do we want to allow the data producer to define
their own concept of grouping (if so this probably wouldn't round trip).

What about singleton features such as SNPs - is a SNP in an intergenic
area a group unto itself? (if so, we shouldn't require the ### directive
after each one)

Note that there's already code for reconstituting the SeqFeature hierarchy
from the ID/Parent tags in Bio::SeqFeature::Tools

Cheers
Chris

On Tue, 23 Nov 2004, Steffen Grossmann wrote:

> Dear Allen, dear Scott,
>
> before we write a next_sequence method, we should have something which
> is able to reconstruct the a set of hierarchically nested features. Any
> suggestions for method names? How about next_group? next_group gives
> back an array of features (which represent the top-level features, the
> lower features appear as subfeatures). A group is ended by a ###
> directive (or by the EOF). A next_sequence method could then also use
> this nesting...
>
> I have ideas how to realize the implementation. Tell me what you think
> about it and I can start doing it.
>
> Steffen
>
> Allen Day wrote:
>
> >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;
> >>        }
> >>
> >>_______________________________________________
> >>Bioperl-guts-l mailing list
> >>Bioperl-guts-l at portal.open-bio.org
> >>http://portal.open-bio.org/mailman/listinfo/bioperl-guts-l
> >>
> >>
> >>
> >_______________________________________________
> >Bioperl-l mailing list
> >Bioperl-l at portal.open-bio.org
> >http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> >
>
>