[Bioperl-l] Modify / Delete features from Bio::Seq object?

[Brian Osborne]

Simon,

As I'm writing I'm looking at Bio::SeqFeature::Generic, where I see a new()
method used, as well as add_sub_SeqFeature() and flush_sub_SeqFeature(). As
I've never written anything using this module I won't claim any particular
understanding of it but I did notice that the script scripts/gff2ps.pl uses
some of these methods, perhaps it would help you. I will add  a note to
bioperl.pod about this script, bioperl.pod should list all scripts and
examples....

Brian O.

----- Original Message -----
From: "simon andrews (BI)" <simon.andrews@bbsrc.ac.uk>
To: "Bioperl (E-mail)" <bioperl-l@bioperl.org>
Sent: Wednesday, January 30, 2002 4:45 AM
Subject: [Bioperl-l] Modify / Delete features from Bio::Seq object?


> I'm trying to put together a script which runs through and EMBL file and
> removes or modifies the features contained within it.  I can parse through
> the features OK, and pick out those I need to deal with, but I can't find
> any methods which allow me to delete or modify existing features (only add
> new ones).
>
> I realise I could do this by creating a new sequence and selectively
copying
> features across, but as these sequences can be big I'd rather just modify
an
> existing one.  Also, I couldn't find a new() method defined in
> Bio::SeqFeatureI.  How do you create a new feature?
>
> In the code below, I'd like to delete each feature / tag whose name is
> currently printed.  I've tried calling undef on those features (hoping
that
> they were references back to the Bio::RichSeq object), but this had no
> effect on the sequence written back out.
>
> Any help is greatly appreciated.
>
> Simon.
>
>
>
> #!/usr/bin/perl -w
> use strict;
> use Bio::SeqIO;
>
> my ($filein,$fileout) = @ARGV;
>
> unless ($fileout){die "Command line is convert [infile] [outfile]\n";}
>
> my $seqio_in = Bio::SeqIO -> new (-format => 'embl',
>   -file => $filein);
>
> my $seqio_out = Bio::SeqIO -> new (-format => 'embl',
>   -file => ">$fileout");
>
> die "Couldn't read $filein\n" unless ($seqio_in);
>
> my $inseq = $seqio_in -> next_seq();
>
> foreach my $feature ($inseq -> all_SeqFeatures()){
>
>   my $tag = $feature -> primary_tag;
>
>   if ($tag eq "exon" or $tag eq "prediction"){
>
>     print "$tag\n"; # Need to remove these features
>
>   }
>
>   elsif ($tag eq 'CDS'){
>
>
>     foreach my $alltag ($feature -> all_tags()){
>
>       if ($alltag eq 'transcript' or $alltag eq 'cds'){
>
> print "\t$alltag\n"; # Need to remove these tags
>
>       }
>     }
>   }
> }
>
> $seqio_out -> write_seq($inseq);
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