[Swift-user] BioInformatics app question

[Alina Bejan]

Hello Ben/Mihael (I guess),

I have a Swift data structure question, which I'll describe below. I am 
trying to write a script that performs the following workflow (example 
below is a computation between a one genome and one genome, i.e. between 
2 .faa files):

formatdb –i Ban.faa
formatdb –i Bce.faa
blastall –p blastp –d Ban.faa –i Bce.faa –m 9 –o out.Bce2Ban.txt
blastall –p blastp –d Bce.faa –i Ban.faa –m 9 –o out.Ban2Bce.txt
simple_reciprocal_best_hits.00.pl –i1 out.Bce2Ban.txt –i2 
out.Ban2Bce.txt –o ortholog.pairs.txt


The 1-1 example works just fine (ortho.swift included) This file also 
works well on multiple OSGEDU sites (that is when I use it with the 
osgedu-sitex.xml included).

I am now trying to scale this up, using a set of 30 genomes (i.e. 
30x30/2 computations - due to symmetry) -- ortho-many.swift included. 
The 30 .faa files are located in the abejan/testBLAST/FASTA directory.

The problem is that I don't find a suitable mapper for this -- Idea is 
that a need to store the intermediate files generated in the formatdb 
step (the .phr, .pin., .psq files) into a structure, and map the 
components of this structure to the newly generated files. Swift 
complains with the way I do it now. Ultimately I would like to run 
'ortho-many' on multiple sites.

Any help is appreciated.

Thanks,
Alina

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