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

[Dimitar Kenanov]

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: dimi...@bii.a-star.edu.sg
tel: +65 6478 8514

[Mark A. Jensen]

Thanks Dimitar-- I'm having a look at the code; will see if I can patch it in.
MAJ

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[Peter]

On Fri, Apr 23, 2010 at 2:02 AM, Dimitar Kenanov
<dimi...@bii.a-star.edu.sg> wrote:
> 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.

There was a bug in fasta34 here which I asked Bill Pearson about
back in May 2008, you can check this on the FASTA mailing list if
you are a subscriber.
https://list.mail.virginia.edu/mailman/listinfo/fasta_list

I was finding even when -O was used, some important information
was still going to stdout. Bill said that the -O support was left over
from when fasta could only do one sequence search at a time. I
don't know if it has been addressed yet, but certainly fasta35 and
fasta36 still put a lot of output on stdout even with the -O option.

I therefore followed his advice and never use -O at all, and instead
always capture stdout.

Peter