Hi all,

I recently upgraded our local instance of galaxy to the latest revision
of galaxy-dist.
Now I tried to use "Extract Genomic DNA" with a 3 column bed file, which
only contains chr, start and end, with database/build set to hg19.

First of all, running the module results in the following error:
--->%---
Traceback (most recent call last):
  File
"/local/data/home/galaxy/galaxy-dist-2011-11-23/tools/extract/extract_genomic_dna.py",
line 283, in <module>
    if __name__ == "__main__": __main__()
  File
"/local/data/home/galaxy/galaxy-dist-2011-11-23/tools/extract/extract_genomic_dna.py",
line 107, in __main__
    seq_path = check_seq_file( dbkey, GALAXY_DATA_INDEX_DIR )
  File
"/local/data/home/galaxy/galaxy-dist-2011-11-23/tools/extract/extract_genomic_dna.py",
line 40, in check_seq_file
    for line in open( seq_file ):
NameError: global name 'seq_file' is not defined
---%<---

I went to the respective file and found that the line which defines
seq_file is commented out:
(l.38 in def check_seq_file())
## seq_file = "%s/alignseq.loc" % GALAXY_DATA_INDEX_DIR

This seems to be a bug in the current version of the file.

Removing the comment, the script tries to check for sequence entries in
alignseq.loc, which I left empty before, since I didn't need aligned
sequences in galaxy until now. Of course this results in another error:

'No sequences are available for 'hg19', request them by reporting this
error.'

I just wanted to raise the question if this dependency is right,
wouldn't one rather like to check for the respective build in faseq.loc
(unfortunately the file format is different, it doesn't contain the seq
in the first column).

Is there a fix for this somewhere already, or did I misunderstand how
this is supposed to work?

Cheers,
Holger




-- 
Dr. Holger Klein
Core Facility Bioinformatics
Institute of Molecular Biology gGmbH (IMB)
http://www.imb-mainz.de/
Tel: +49(6131) 39 21511
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