[Bioperl-l] more genewise

[Chris Fields]

Dimitar,

It would be better if you could create a bug report describing the problem (with minimal example data and code) and provide a diff file or patch.  This gives us a chance to do some code review and commit the patch if it passes tests.

Here's a HOWTO on this:

http://www.bioperl.org/wiki/HOWTO:SubmitPatch

Let us know when it's submitted and we can take a look.

chris

On May 7, 2010, at 12:03 AM, Dimitar Kenanov wrote:

> 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
> 
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