[Bioperl-l] Parsing output INFERNAL 1.0.2

Estefania soyestepi at gmail.com
Tue Aug 7 15:28:58 EDT 2012


Dear all, I have some problems parsing INFERNAL 1.0.2 ouput.
Using this script (previously cited here), nothing is printed and I have no
errror messages.
#!/usr/bin/perl -w
use strict;use Data::Dumper;
use Bio::SearchIO;

my $infile = $ARGV[0];                  # infernal report
my $parser = Bio::SearchIO->new(-format => 'infernal',
                                                   -file => $infile);
while( my $result = $parser->next_result ) {
      print $result->query_name . "\n";
}

If I try to print other elements, the only ones I can print
are:$parser->algorithm(), $parser->version(),
and for: $result = $parser->next_result, it works just for $size =
$result->database_letters() and  $dbname = $result->database_name() (but
displays wrong name)

Is this a problem of the version of Infernal? How can I parse this output?
I also have tabulated output.
Thanks in advance
estepi


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