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

[Andrew Nunberg]

 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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