[Bioperl-l] Parsing output INFERNAL 1.0.2

Mark Aquino maquino at knome.com
Tue Aug 7 20:16:56 EDT 2012


Try changing the use to Bio::SeqIO::Infernal and see if that works. 

Sent from my iPhone

On Aug 7, 2012, at 3:30 PM, "Estefania" <soyestepi at gmail.com> wrote:

> 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
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 




More information about the Bioperl-l mailing list