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// Getting top 10 sequences of BLAST results Bio Python
// July 5, 2011 at 12:31 AM

http://stackoverflow.com/questions/6577975/getting-top-10-sequences-of-blast-results-bio-python
I want to get top 10 sequences of BLAST results (just the sequences, no alignment or score or e-value etc). I am inputting a text file containing 5 fasta file. So my output should be top 10 blast hits of each fasta file.. therefore my output file will have 50 sequences.

I am reading each of my input fasta file through Bio.SeqIO, writing it as temp.faa and then passing it to command line BLAST through subprocess as

blastp -db nr -query temp.faa -out out.faa -evalue 0.001 -gapopen 11 -gapextend 1 -matrix BLOSUM62 -remote -outfmt 2


the output has lots of other information. Should I parse this output now or there's a better way.

Thanks

P.S XML might be a way but I didn't find a relavant NCBIXML parser syntax.


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