[EMBOSS] jaspscan - multiple sequences

[ajb at ebi.ac.uk]

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
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>
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