[Bioperl-l] BLAST parsing Question
Simon K. Chan
Wed, 8 May 2002 18:45:23 -0700 (PDT)
My fellow BioPerl-ers,
It took me a couple of hours to realize that what I
need to do is EXTREMELY common and that it's already
been done. D'oh!! :-0
So, I made a fasta database by using the formatdb
command. I have a fasta file with a bunch of
fasta file: seq A, seq B, seq C
db made with formatdb: seq 1, seq 2, seq 3
I blast the sequences in the file against the
So, let's say that seq A only hits seq 1 with a P
value of 10e-100 and seq B only hits seq 1 with a P
value of 2e-15. Seq C hits nothing. How would I pull
out that Seq A matches Seq1 and that Seq C AND Seq B
I tried to do this with hashes where the keys were the
matches from the db and the values were arrays with
the P value and query name. But it go real messy.
Yuck! Does anyone know of a module or some other
quick way of doing this?
Simon K. Chan - firstname.lastname@example.org
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