[Bioperl-l] Bio::SeqIO HOWTO

[Barry Moore]

Li-

You don't need to modify the script.  It is written to accept the
filename and format on the command line like this:  perl getaccs.pl
mouse.fasta fasta.

Barry

> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org [mailto:bioperl-l-
> bounces at portal.open-bio.org] On Behalf Of chen li
> Sent: Tuesday, November 01, 2005 10:30 PM
> To: bioperl-l at bioperl.org
> Subject: [Bioperl-l] Bio::SeqIO HOWTO
> 
> Hi folks,
> 
>  Here is one script copied from the Bio::SeqIO HOWTO:
> 
>      use Bio::SeqIO;
>      my $usage = "getaccs.pl file format\n";
>      my $file = shift or die $usage;
>      my $format = shift or die $usage;
> 
>      my $inseq = Bio::SeqIO->new('-file'  => "<$file",
>               '-format' => $format );
>      while (my $seq = $inseq->next_seq) {
>            print $seq->accession_number,"\n";
>      }
>      exit;
> 
> 
> I have a small file called mouse.fasta kept in the
> same directory. My question is that  how does the
> script know to read in mouse.fasta? Where should I
> make a small modification in the script?
> 
> Thanks,
> 
> Li
> 
> 
> 
> 
> 
> 
> 
> __________________________________
> Yahoo! FareChase: Search multiple travel sites in one click.
> http://farechase.yahoo.com
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l