[Bioperl-l] more genewise

[Dimitar Kenanov]

Hi guys,
another question about genewise. Is it possible to get the query seq and 
the protein translation of the target seq somehow?

So, up to now i could not find a way to get the percent identity between 
query and target(the protein translation)  :(     I spent some time on 
CPAN and perldoc and even checked the code of several modules but still 
no solution. Then i decided to extract the sequences out of the output 
file and compare them somehow but i could not find a way and for that. I 
found that the module 'Bio::Tools::Run::Genewise' is creating internal 
temp output file which i cant access so i can parse it myself and 
extract whatever.

Because with current implementation i cant access that temp output i 
hacked a bit 'Bio::Tools::Run::Genewise' so i can pass my output file to 
the constructor, like that:

     my $factory = Bio::Tools::Run::Genewise->new( output => $tmpout); 
#not "-output" cos the module currently doesnt like it

I modified the BEGIN section and the '_run' subroutine. My lines and the 
originals are marked :
--------------
BEGIN {
     @GENEWISE_PARAMS = qw( DYMEM CODON GENE CFREQ SPLICE GENESTATS INIT
                SUBS INDEL INTRON NULL INSERT SPLICE_MAX_COLLAR 
SPLICE_MIN_COLLAR
          GW_EDGEQUERY GW_EDGETARGET GW_SPLICESPREAD
                KBYTE HNAME ALG BLOCK DIVIDE GENER U V S T G E M);

     @GENEWISE_SWITCHES = qw(HELP SILENT QUIET ERROROFFSTD TREV PSEUDO 
NOSPLICE_GTAG
                             SPLICE_GTAG NOGWHSP GWHSP
                 TFOR TABS BOTH HMMER );

     $OK_FIELD{OUTPUT}++; *#dimitar
*    # Authorize attribute fields
     foreach my $attr ( @GENEWISE_PARAMS, @GENEWISE_SWITCHES,
                        @OTHER_SWITCHES) { $OK_FIELD{$attr}++; }
}
-----------------------
-----------------------
   my ($tfh1,$outfile1) = $self->io->tempfile(-dir=>$self->tempdir);
     $self->debug("genewise command = $commandstring");
     my $outfile2=$self->output; *#dimitar*
  #   my $status = system("$commandstring > $outfile1"); *#original*
     my $status = system("$commandstring > $outfile2 "); *#dimitar*
     $self->throw("Genewies call $commandstring crashed: $? \n") unless 
$status==0;

#    my $genewiseParser = Bio::Tools::Genewise->new(-file=> $outfile1); 
*#original*
     my $genewiseParser = Bio::Tools::Genewise->new(-file=> $outfile2); 
*#dimitar*
-----------------------

More the method 'cds' from 'Bio::SeqFeature::Gene::Exon/I' gives nothing 
back it doesnt matter what i tried. And i tried a lot :) Fortunately for 
me i dont need that for now. But tried and didnt work so had to say.

Cheers
Dimitar

-- 
Dimitar Kenanov
Postdoctoral research fellow
Protein Sequence Analysis Group
Bioinformatics Institute
A*STAR, Singapore
tel: +65 6478 8514