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

Dimitar Kenanov dimitark at bii.a-star.edu.sg
Thu Apr 22 21:02:31 EDT 2010

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 :)


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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