[Bioperl-l] Parsing output INFERNAL 1.0.2

Fields, Christopher J cjfields at illinois.edu
Wed Aug 15 11:50:06 EDT 2012


Mark, no, the parser is Bio::SearchIO-based.  My guess is this is a legitimate bug, Infernal 1.0.2 is the latest release and it is very possible there was a format change that is breaking things.  

Estepi, can you send me an example file to test?  I know Infernal was recently updated and is much faster, I want to make sure BioPerl parses it correctly.

chris

On Aug 7, 2012, at 7:16 PM, Mark Aquino <maquino at knome.com> wrote:

> 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
>> 
> 
> 
> _______________________________________________
> 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