[Bioperl-l] problem with SeqIO.pm

[Ewan Birney]

On Mon, 28 Jan 2002, Brian Osborne wrote:

> Simon,
> 
> I'll amend the description of desc() in Seq.pm to be a bit more descriptive.
> Also, you should expect the documentation that will appear in version 1.0 of
> bioperl to be more detailed, particularly for this key module.
> 

Go Brian!



> Brian O.
> 
> ----- Original Message -----
> From: "Simon Chan" <schan@xenongenetics.com>
> To: <bioperl-l@bioperl.org>
> Sent: Monday, January 28, 2002 1:12 PM
> Subject: [Bioperl-l] problem with SeqIO.pm
> 
> 
> > Hey All,
> >
> > Let's say I want to parse a FASTA file and I want to fish out all the
> headers.
> > So, if my file looks like this:
> >
> > > exon_name (Simon's Data - Hand's off!)
> > NNNNNNNNNNNNNNNNNNNNNNNN
> > NNNNNNNNNNNNNNNNNNNNNNNN
> > etc.
> >
> > The following code only returns to me "exon_name" and not the part in
> brackets.  So, it seems that not the whole header is being returned.
> >
> > my $input= Bio::SeqIO->newFh(-file => "$input " , -format => "$format");
> >
> > while (my $info = <$input>){
> >
> >
> >     push (@header, $info->display_id());
> >     push (@bases ,$info->seq());
> >
> > }
> >
> >
> > I read over the doc for this module and did not fine anything helpful.
> The problem can be avoided if you just read in the input via a good old
> fashion <FILEHANDLE>, but I was taught that an efficient programmer is also
> a lazy programmer!  ;-)
> >
> > Thanks for your time, All.
> >
> > ##############################
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> > Bioperl-l@bioperl.org
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> >
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