[Bioperl-l] Question about Fgenesh.pm

[Chris Dwan]

Sorry about the lack of quality checking.  I would love to help, but I 
no longer have access to fgenesh to do such testing (licensed program, 
new employers don't own it).

-Chris Dwan
The Bioteam

On Jul 23, 2004, at 1:31 PM, Jason Stajich wrote:

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