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

Chris Fields cjfields at illinois.edu
Fri Apr 16 07:32:35 EDT 2010


You should always forward bioperl-related matters directly to the mail list.  Unfortunately I'm unavailable until Monday, so I can't immediately get to it.  Can anyone take a look at this in the meantime?


Begin forwarded message:

> From: Dimitar Kenanov <dimitark at bii.a-star.edu.sg>
> Date: April 15, 2010 11:45:44 PM CDT
> To: Chris Fields <cjfields at illinois.edu>
> Subject: about Bio::Tools::Run::Alignment::StandAloneFasta
> Hi Chris,
> i wrote you 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 theres 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 attache the my 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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