Bioperl: Help with blast and vector trimming
Tue, 02 Feb 1999 17:20:44 -0500
Thanks, Steve, I figured this out yesterday.
Perhaps you can use $^X (aka $EXECUTABLE_NAME) in a future version when
invoking this program, to assure correct processing. I'll experiment with
this and contact you off-list with the results.
The good news is, this is the only instance of this problem which I found
when I searched for such strings in the code.
At 02:10 PM 2/2/99 -0800, Steve Chervitz wrote:
>Jonathan Epstein writes:
> > I'm trying to use the bioPerl blast functionality, initially for trimming
> > vector from some EST's.
> > When I run the sample:
> > perl ./blast_seq.pl seq/seqs.fasta -eid -prog blastp -db yeast -signif
> > 1e-5 -table 2 >runseqs.out
> > I encounter the following error, even though the named file exists.
> > UX:sh (sh): ERROR:
> > Not found
> > No Blast results saved.
>Try changing the #! line of postclient.pl to /usr/bin/perl instead of
>/usr/local/bin/perl (if your perl executable is not reachable via
Jonathan Epstein Jonathan_Epstein@nih.gov
Unit on Biologic Computation (301)402-4563
Office of the Scientific Director Bldg 31, Room 2A31
Nat. Institute of Child Health and Development 31 Center Drive
National Institutes of Health Bethesda, MD 20892
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