[Bioperl-l] maf.pm

Jason Stajich jason at bioperl.org
Fri Jan 23 18:08:58 EST 2009


Iterate through the sequences, here is code that just prints out the  
sequence ID and description:

while(my $aln = $in->next_aln ) {
for my $seq ( $aln->each_seq ) {
   print $seq-id, " ", $seq->description, "\n";
  }
}

On Jan 23, 2009, at 1:42 PM, charles denby wrote:

> I'm using maf.pm to read .maf formatted files downloaded from the UCSC
> database.
> I want to know how to retrieve the species, chromosomal position start
> and end of a given alignment (Bio::AlignIO object).
> Any help would be much appreciated.
> Thanks
> Charles
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



More information about the Bioperl-l mailing list