[Bioperl-l] Parsing EMBOSS::needle output

Ryan Golhar golharam at umdnj.edu
Tue Jul 26 12:05:51 EDT 2005

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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