FW: [Bioperl-l] Question about Fgenesh.pm

[Jason Stajich]

Done - would be good to have some parsing for FGENESH as well.  If someone
would volunteer that would be great.

-jason

On Fri, 23 Jul 2004, Andrew Nunberg wrote:

>
>  On 7/23/04 11:58 AM, "Andrew Nunberg" <anunberg at oriongenomics.com> wrote:
>  Sorry I figured it out
>  The parsing  of the seqid was incorrect
>  line 375 has
>    if(/^Seq name:\s+(\S+)/) {
>        $seqname = $1;
>        next;
>    }
>  The regex should be changed to /\s+Seq name:\s+(\S+)/
>  That fixes my problem since I can get the info from seq_id rather than from
>  analysis_subject
>
>
> >> Hi,
> >> I am trying to parse an fgenesh analysis file using Bio::Tools::Fgenesh from
> >> bioperl-live
> >>
> >> I  had to make a change in the module at line 320
> >> from:
> >>   $predobj->primary_tag($ExonTags{$flds[3]} . 'Exon');
> >>
> >> to:
> >>   $predobj->primary_tag($ExonTags{$flds[4]} . 'Exon');
> >>
> >> For the parser to work.
> >>
> >> I then wish to retreive the name of the dna sequence that was fed to the
> >> parser using the analysis_subject/query method
> >>
> >> $fgenesh = Bio::Tools::Fgenesh->new(-file=>"results file");
> >> $gene = $fgenesh->next_prediction;
> >>
> >> $fgenesh->analysis_subject;
> >>
> >> This method returns undef, although it appears in the code that the info is
> >> stored there.
> >> Lines 366-373 from Fgenesh.pm
> >> if(/^(FGENESH)\s+([\d\.]+)/) {
> >>       $self->analysis_method($1);
> >>       $self->analysis_method_version($2);
> >>           if (/\s(\S+)\sgenomic DNA/) {
> >>             $self->analysis_subject($1);
> >>           }
> >>       next;
> >>   }
> >> Any input would be appreciated
> >
> > --
> > Andrew Nunberg
> > Bioinformagician
> > Orion Genomics
> > (314)-615-6989
> > www.oriongenomics.com
> >
>
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>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu