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

[Allen Day]

On Tue, 23 Nov 2004, Chris Mungall wrote:

> 
> Is a group defined as a set of connected features?

i interpret group to mean a set of items, each of which has 0..N
conections to other members of the set, and 0 connections to members in
other sets.

> 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).

on a related note, maybe Bio::FeatureIO::GFF should (optionally) write a
'###' into the filehandle after each time write_feature() is called.

> 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)

how does an intergenic snp differ from a genic snp?  is there an easy way
via SO to identify features that should never be connected to others?  
can we rely on Bio::SeqFeature::Tools to do this for us?

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

-allen

> 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;
> > >>        }
> > >>
> > >>_______________________________________________
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> > >>Bioperl-guts-l at portal.open-bio.org
> > >>http://portal.open-bio.org/mailman/listinfo/bioperl-guts-l
> > >>
> > >>
> > >>
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