Hi,
Thanks for the patch! Works like a charm.
jorrit
On Aug 4, 2008, at 5:50 PM, [EMAIL PROTECTED] wrote:
Dear Jorrit,
It was an oversight. The attached patch file should fix the
source code - it was created a while ago to help someone who
asked the same question. Go into the EMBOSS-6.0.1 directory and type:
gunzip -c /somewhere/jaspscan-patch.gz | patch -p1
then recompile. I am away at the moment but one of my colleagues
will be
able to answer any further questions on this. The attached will become
part of an official patch sometime after I get back.
Alan
Dear all,
I have only today found and installed EMBOSS on an OSX10.4 computer,
because I wanted to use jaspscan to feed multiple sequences to the
JASPAR database at once. The tool seems to work alright, except when
I try to enter multiple fasta sequences in one go. It analyzes/writes
only the first seq and then exits with:
EMBOSS An error in jaspscan.c at line 763:
Cannot open matrix file <null>
I could maybe write a script that feeds sequences one after one, but
I'd like to do it the cleaner way.
Now, since I am very new to EMBOSS, I might be doing something very
obvious wrong. Basically I do:
$ jaspscan
Scans DNA sequences for transcription factors
Input nucleotide sequence(s): test?.seq
Jaspar matrix set
C : Core
F : Fam
P : Phylofacts
N : CNE
O : POLII
S : SPLICE
Matrix set [C]:
Comma separated matrix list [all]:
Threshold percentage [80.0]:
Output report [fasta_test.jaspscan]:
And I have two files called test1.seq and test2.seq, which are both
fasta formatted files. Each one can be analyzed in a single-file
session, but there seems to be an error when processing the two of
them. If anyone has an idea how to get this working I'd love to
hear it.
Cheers,
jorrit
--
Jorrit Boekel
Ph.D. student
Dept. of Neuroscience
Karolinska Institutet
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<jaspscan-patch.gz>
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