[Bioperl-l] Problem using StandAloneFasta about 80000 times...

[Jason Stajich]

sounds like problems that people have had for StandAloneBlast in the past.
I went through StandAloneBlast with as much of a fine tooth comb as I
could bear and made sure filehandles and program handles were closed.
You may have to do this in StandAloneFasta as I don't think it has had
this type of attention. It should be submitted as a bug for someone to
track down (desperately seeking volunteers to help with bug
fixing/tracking down...)

Alternatively If you don't want to do this - can you write your
program to generate the whole input file list for FASTA and then just run
this as a single input to FASTA at the end?

-jason

On Thu, 24 Jul 2003, Palle Villesen wrote:

> Hi,
>
> I've made small program for running FASTA chromosomal coordinates
> against other chromosomal coordinates (basically a simple test for
> repeated sequence (LTR))...
>
> Everything runs smoothly except I get a STACK error after 1019 runs.
>
> 1016    485     X       19107183        19107980        YES
> 19102529        19102843        19111836        19112151        314
> 9307    0.78    5.4e-150
> 1017    484     X       20157010        20158151        NO
> 1018    483     X       20543945        20544912        NO
> 1019    482     X       20582210        20583516
> ------------- EXCEPTION  -------------
> MSG:
> STACK Bio::Tools::Run::Alignment::StandAloneFasta::run
> /a/home/serine/palle/bioperl-run/Bio/Tools/Run/Alignment/StandAloneFasta.pm:336
>
> I looked in the code (StandAloneFasta.pm) and found that it opens a
> FASTARUN handle on line 336, and I couldn't find a close FASTARUN
> anywhere, but since I'm still a rookie in perl I'm just confused...
>
> If I wrap my small program, so it is executed thousands of times, it
> works... It's only when running the StandAloneFasta module directly I
> get the error...
>
> Any help will be appreciated,
> Palle
> BiRC.dk
>
>
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu