Bioperl: Help with blast and vector trimming

Jonathan Epstein
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.

- Jonathan

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 ./ 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 to /usr/bin/perl instead of
>/usr/local/bin/perl (if your perl executable is not reachable via

Jonathan Epstein                      
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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