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

Chris Fields cjfields at illinois.edu
Tue Aug 9 16:10:37 EDT 2011


Following this up: Nadine, did you have a bug to report?  It's kind of hard to fix this without some example data.

chris

On Aug 3, 2011, at 8:10 AM, Chris Fields wrote:

> 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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> 
> 
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