[Bioperl-l] embl parser to extract exon lengths from feature table (FT)

[Hilmar Lapp]

> -----Original Message-----
> From: Hilmar Lapp 
> Sent: Friday, September 27, 2002 9:55 AM
> To: Zayed Albertyn; bioperl-l@bioperl.org
> Subject: RE: [Bioperl-l] embl parser to extract exon lengths from
> feature table (FT)
> 
> 
> 
> use Bio::SeqIO;
> 
> my $seqin = Bio::SeqIO->new(-file => "<myinputfile", -format 
> => "embl");
> 
> while(my $seq->next_seq()) {
           ^^^^^^^^^^^^^^

Sorry, this line needs to read

while(my $seq = $seqin->next_seq()) {


> 	foreach my $feat ($seq->top_SeqFeatures()) {
> 		next unless $feat->primary_tag() eq "mRNA";
> 		my $i = 1;
> 		foreach my $loc ($feat->location()->each_location()) {
> 			print $seq->display_id(), 
>                         ": exon $i has length ", $loc->length(),"\n";
> 		      $i++;
> 		}
> 	}
> }
> 
> This will work for single-exon, multi-exon, plus-strand, and 
> reverse-strand. It will even work for remote-location exons.
> 
> 	-hilmar
> 
> > -----Original Message-----
> > From: Zayed Albertyn [mailto:zayed@sanbi.ac.za]
> > Sent: Friday, September 27, 2002 2:25 AM
> > To: bioperl-l@bioperl.org
> > Subject: [Bioperl-l] embl parser to extract exon lengths 
> from feature
> > table (FT)
> > 
> > 
> > Hi there
> > 
> > I would like to know if there is a quick and neat way in perl 
> > or bioperl
> > to extract the lengths of exons from FT in EMBL format e.g.
> > 
> > FT   mRNA
> > complement(join(501..977,1182..1358,3721..3871,6060..6147,
> > FT                   8480..8591))
> > FT                   /note=EST2genome
> > FT                   /evidence=EXPERIMENTAL
> > 
> > 
> > All I would like are the lengths. I could write a script to 
> > do this but
> > somehow I feel that it has already been done in bioperl.
> > 
> > Thanks
> > Zayed
> > 
> > 
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> > 
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