[Bioperl-l] Bio::Tools::Fgenesh bug? and fix?

[Cook, Malcolm]

Got it.

Commits made.

Thanks for the history lesson.

Cheers,

Malcolm Cook
 

>-----Original Message-----
>From: Christopher Dwan [mailto:chris at dwan.org] 
>Sent: Monday, July 10, 2006 9:07 PM
>To: Cook, Malcolm
>Cc: bioperl-l
>Subject: Re: Bio::Tools::Fgenesh bug? and fix?
>
>
>I'm not surprised that there are parts that don't work right, I coped  
>genscan.pm and made the absolute minimal changes required to get what  
>I needed working.  Haven't touched it since.
>
>Please feel free to do what needs to be done, and sorry about the mess.
>
>-Chris Dwan
>
>On Jul 10, 2006, at 8:25 PM, Cook, Malcolm wrote:
>
>> I am finding the Bio::Tools::Fgenesh parser to incorrectly handle the
>> feature coordinates on - strand predictions.
>>
>> In particular, start & end are deliberately reversed if the strand is
>> '-'.
>>
>> I guess this was a holdover from Genscan.pm and wasn't really tested
>> !?!?!
>>
>> Or, perhaps fgenesh v 2.4 which I am running has different output in
>> this respect compared to the version 2.0, against which this module  
>> was
>> written.
>>
>> Or, perhaps my understanding is blotto (known to happen).
>>
>> Does anyone know for sure?
>>
>> If I comment out selected lines...
>>
>> #	    if($predobj->strand() == 1) {
>> 		$predobj->start($start);
>> 		$predobj->end($end);
>> #	    } else {
>> #		$predobj->end($start);
>> #		$predobj->start($end);
>> #	    }
>>
>> ... then GFF produced by my naive fgenesh2gff script below is correct
>> (at least w.r.t. strand and coordinates - GFF compatibility purists
>> might wince).
>>
>> Should I commit this change to head?
>>
>>
>> Malcolm Cook
>> Database Applications Manager, Bioinformatics
>> Stowers Institute for Medical Research
>>
>>
>>
>> #!/usr/bin/env perl
>>
>> # fgenesh2gff
>> # PURPOSE: parse fgenesh output into gff
>> # USAGE: fgenesh fish somefish.dna | fgenesh2gff >
>> somefish.dna.fgenesh.gff
>>
>> use strict;
>> use warnings;
>> use Bio::Tools::Fgenesh;	
>> use Bio::FeatureIO;
>>
>> # Remaining options should name files to process, but if 
>none, process
>> # standard input:
>> @ARGV = ('-') unless @ARGV;	
>> my $fgenesh = Bio::Tools::Fgenesh->new(-fh => \*ARGV);
>>
>> my $featureout =   new Bio::Tools::GFF(
>> 				       -gff_version => 2, #whatever ;)
>> 				      );
>> my $IDNUM = 0;
>> while (my $gene = $fgenesh->next_prediction()) {
>>   my $ID =  "fgenesh" . ++ $IDNUM;
>>   $gene->add_tag_value('ID', $ID);
>>   $featureout->write_feature($gene);
>>   foreach ($gene->exons()) {
>>     $_->add_tag_value('Parent', $ID);
>>     $_->seq_id($gene->seq_id);
>>     $featureout->write_feature($_);
>>   }
>> }
>> $fgenesh->close();
>>
>> exit 0;
>>
>
>