[EMBOSS] jaspscan - multiple sequences

[Jorrit Boekel]

Hi,

Thanks for the patch! Works like a charm.

jorrit

On Aug 4, 2008, at 5:50 PM, ajb at ebi.ac.uk 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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>> EMBOSS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/emboss
>>
>> <jaspscan-patch.gz>