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

[Steffen Grossmann]

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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>>
>>    
>>
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>  
>

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