[Bioperl-l] Question to Bio::SearchIO::infernal.pm

Chris Fields cjfields at illinois.edu
Wed Aug 3 09:10:20 EDT 2011


Nadine,

Hard to guess w/o seeing the report, but I'm not terribly surprised.  I believe I only coded for simple 1 CM reports, IIRC.  You'll have to file this as a bug on redmine along with an example.  

chris

On Jul 29, 2011, at 9:35 AM, Nadine Elpida Tatto wrote:

> Hi There!
> 
> 
> 
> I was wondering if you would or can help me.
> 
> 
> I have an infernal report containing about 2000 CMs from an infernal run against Rfam.cm. To parse this report I wanted to use Bio::SearchIO::infernal.pm. Unfortunately this turned out to be a problem for me, because "$parser->next_result" only delivers the result for the first CM in the report and nothing more. 
> 
> 
> My code:
> #!/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 $result->query_name . "\n";
> }
> 
> 
> exit;
> 
> 
> 
> 
> The output: 
> 
> 
> ntatto:~$ ./infernalParser.pl  infernal.output
> 5S_rRNA
> ntatto:~$ 
> 
> 
> 
> 
> I would expect the following (like parsing a blast report):
> 
> 
> ntatto:~$ ./infernalParser.pl  infernal.output
> 5S_rRNA
> 5_8S_rRNA
> U1
> ...
> ntatto:~$ 
> 
> 
> 
> I would be glad for help.
> 
> 
> Thank you in advance.
> 
> 
> Best Regards
> 
> 
> N Tatto
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
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