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 > > > > > _______________________________________________ > EMBOSS mailing list > [email protected] > http://lists.open-bio.org/mailman/listinfo/emboss >
jaspscan-patch.gz
Description: GNU Zip compressed data
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