[Bioperl-l] Parsing EMBOSS::needle output

Barry Moore bmoore at genetics.utah.edu
Tue Jul 26 16:56:11 EDT 2005


This works for me with my own sequence files.  I don't know if your
mailer line wrapped your script, but when I copied your script I had to
fix the '-gapopen' parameter in your needle command line.  You can't
have any whitespace between the '-' and 'gapopen'.  Did you check to be
sure that /tmp/compare.needle was actually written?  If you still have
trouble, you can send along the files that your comparing, and I'll see
if they run for me.


-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Ryan Golhar
Sent: Tuesday, July 26, 2005 10:06 AM
To: 'Bioperl List'
Subject: [Bioperl-l] Parsing EMBOSS::needle output

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

Any ideas?


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