[Bioperl-l] blast output -> blast -m8 output

Jason Stajich jason.stajich at duke.edu
Tue Jan 3 22:45:10 EST 2006

The existing search2table script in scripts/searchio does this for  
you - I don't think there is a writer plugin but there could be.

Note that if you just using BLAST you will find that the blast2table  
script that is included in the BLAST book (see the O'Reilly website  
for the book and download the code examples) will also generate this  
sort of thing for you and will be many times faster than SearchIO  
code.  There is also an equivalent hmmer_to_table and  
fastam9_to_table which are very fast re-formatters that don't  
actually use SearchIO since one is just trying to get the very simple  
data out.

$ more scripts/searchio/search2table.PLS
=head1 NAME

search2table - turn SearchIO parseable reports into tab delimited  
format like NCBI's -m 9


   search2table -f fasta -i file.FASTA -o output.table

On Dec 29, 2005, at 8:30 PM, Torsten Seemann wrote:

> Amir Karger wrote:
>> I'm writing a script that will take regular blast output and  
>> translate it to
>> blast -m8 tabular form. (The reverse transform won't work without  
>> re-doing
>> the alignments.)
>> I've attached the blast output for running 3 sequences against  
>> month.aa.
>> Below are the script, the script output, and the blast -m8 output.  
>> (Output
>> is the same for bioperl-1.4 and 1.5-RC1.)
> I can't verify that your code is correct, but I have two comments  
> anyway which other BioPerl developers may be able to help us with:
> 1. Can this be done already using any of the Writer modules?
> http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/ 
> SearchIO/Writer/toc.html
> 2. If not should probably turn the code into a blasttableWriter.pm  
> class?
> -- 
> Torsten Seemann
> Victorian Bioinformatics Consortium, Monash University, Australia
> http://www.vicbioinformatics.com/
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> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
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Jason Stajich
Duke University

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