[Bioperl-l] Question about Fgenesh.pm

[Jason Stajich]

$lastcomment =~ 's/some parsing/some parsing testing, i.e. the test suite/';

On Fri, 23 Jul 2004, Andrew Nunberg wrote:

> On 7/23/04 12:25 PM, "Jason Stajich" <jason at cgt.duhs.duke.edu> wrote:
> What do you mean, this is parsing for FGENESH.. ???
>
> > 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
> >>>
> >>
> >> ------ End of Forwarded Message
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at portal.open-bio.org
> >> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >
> > --
> > Jason Stajich
> > Duke University
> > jason at cgt.mc.duke.edu
> >
>
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu