[Bioperl-l] producing an organism report from BLAST results?
jason.stajich at duke.edu
Mon Nov 21 16:26:23 EST 2005
Well isn't encoded in the hit name?
my ($gi) = ($hit->name =~ /gi\|(\d+)/ );
If you run WU-BLAST you need to provide the -gi option on the command
If you run NCBI-BLAST you need to provide the -I option
From the blastall help:
-I Show GI's in deflines [T/F]
default = F
On Nov 21, 2005, at 4:22 PM, Tim Reid wrote:
> You need to look up the taxonomid ID from the gi number for a record.
> thanks for your reply, but i am unable to find the gi number of a
> blast hit.
> i have looked at the each_accession_number method in
> Bio::Search::HitI, but it does not appear to yield a gi number.
> your help is appreciated.
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