[Bioperl-l] want score from needle output

neeti somaiya neetisomaiya at gmail.com
Wed Jan 31 05:25:33 EST 2007


Hi,

I am using a code like the following to parse needle output. While I am able
to get the percent identity value, the score method is not returning
anything, though the needle output does report a score too.

--------------------------------
my $str = Bio::AlignIO->new(-format => 'emboss',-file => $needle_output);
my $aln = $str->next_aln();

my $aln_perc_iden = $aln->percentage_identity;
my $aln_score = $aln->score;
-----------------------------

Can anyone suggest what the problem could be?

-- 
-Neeti
Even my blood says, B positive


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