[Bioperl-l] about Bio::Tools::Run::Alignment::StandAloneFasta

Mark A. Jensen maj at fortinbras.us
Thu Apr 22 23:05:27 EDT 2010

Thanks Dimitar-- I'm having a look at the code; will see if I can patch it in.
----- Original Message ----- 
From: "Dimitar Kenanov" <dimitark at bii.a-star.edu.sg>
To: <bioperl-l at bioperl.org>
Sent: Thursday, April 22, 2010 9:02 PM
Subject: [Bioperl-l] about Bio::Tools::Run::Alignment::StandAloneFasta

> Hi guys,
> i am sorry for the repeating but i was told to post it on the list. So
> below is
> what was my problem and how i solved it for me:
> I wrote about that the 'q' option in the module
> 'Bio::Tools::Run::Alignment::StandAloneFasta' is not functioning. I
> found out important thing. When 'ssearch' is used from terminal with -O
> (for the output) then there is always output and on the terminal. The only
> way to avoid that is to use '>' to direct to output to a file. So i went
> back to the module and modified it a bit :) Now i can give to the module
> the 'O' option as usual with my output file plus the 'q' option and i
> dont get output on the terminal.
> I just modified the '_setparams' and 'run' functions a bit. I attach
> the modified module file where i commented the original lines with
> 'original' (very original :) ) and the others with 'dimitar'. There is
> the '$dim_out' = dimitar output :) to be clear and not to clash with
> something else.
> May be there are some other users who dont want to see much output :)
> Cheers
> Dimitar
> -- 
> Dimitar Kenanov
> Postdoctoral research fellow
> Protein Sequence Analysis Group
> Bioinformatics Institute
> A*STAR, Singapore
> email: dimitark at bii.a-star.edu.sg
> tel: +65 6478 8514


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