[Bioperl-l] problem with SeqIO.pm

[Brian Osborne]

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.

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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