[Bioperl-l] Parsing EMBOSS::needle output

[Jason Stajich]

I think the "emboss" format changed in 3.0.0
solutions:
a) fix the AlignIO::emboss parser to handle both flavors (old and new)
b) have it output MSF format and use AlignIO::msf.

-jason
On Jul 26, 2005, at 9:05 AM, Ryan Golhar wrote:

> I'm trying to parse the output of EMBOSS::needle (EMBOSS 3.0.0) using
>
> `needle -asequence /tmp/genbank.cds -bsequence ../Seq/$tuple/$organism 
> -
> gapopen 10 -gapextend 0.5 -outfile /tmp/compare.needle 2>/dev/null`;
>
> my $alnobj = new Bio::AlignIO(-format => 'emboss',
>                               -file   => '/tmp/compare.needle');
> my $alignment = $alnobj->next_aln;
> print "\tPercentage Identity: ", $alignment->percentage_identity, "\n";
>
> However $alignment never gets defined.  $alnobj never returns an
> alignment object.   I saw other posts relating to this but not
> solutions...
>
> Any ideas?
>
> Ryan
>
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--
Jason Stajich
http://www.duke.edu/~jes12
jason.stajich -at- duke.edu