Question: Extract MAF not working - NameError
0
gravatar for ana16
2.5 years ago by
ana1620
ana1620 wrote:

Hello all,

I am unable to extract MAF files from a set of genomic intervals. I was previously able to do this (last week) but after the release of the new version I couldn't do this again. I have seen posts on biostars reporting similar problems, but none yet related to MAF tools.

The error I am getting is:

Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/tools/maf/interval2maf.py", line 142, in <module>
    __main__()
  File "/cvmfs/main.galaxyproject.org/galaxy/tools/maf/interval2maf.py", line 112, in __main__
    for block in index.get_as_iterator( src, region.start, region.end ):
  File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/bx/interval_index_file.py", line 167, in get_as_iterator
    for block, index, offset in self.get_as_iterator_with_index_and_offset( src, start, end ):
  File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/bx/interval_index_file.py", line 171, in get_as_iterator_with_index_and_offset
    for block, idx, offset in index.get_as_iterator_with_index_and_offset( src, start, end ):
  File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/bx/interval_index_file.py", line 249, in get_as_iterator_with_index_and_offset
    yield self.get_at_offset( val ), self, val
  File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/bx/interval_index_file.py", line 254, in get_at_offset
    return self.read_at_current_offset( self.f, **self.data_kwargs )
  File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/bx/align/maf.py", line 37, in read_at_current_offset
    return read_next_maf( file, **kwargs )
  File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/bx/align/maf.py", line 136, in read_next_maf
    line = readline( file, skip_blank=True )
  File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/bx/align/maf.py", line 201, in readline
    line = file.readline()
  File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/bx/misc/seeklzop.py", line 117, in readline
    self.fix_dirty()
  File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/bx/misc/seeklzop.py", line 77, in fix_dirty
    self.current_block = StringIO( self.load_block( chunk ) )
  File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/bx/misc/seeklzop.py", line 69, in load_block
    value = lzo.decompress( data )

NameError: global name 'lzo' is not defined

Thanks in advance!

galaxy maf • 697 views
ADD COMMENTlink modified 2.5 years ago by Jennifer Hillman Jackson25k • written 2.5 years ago by ana1620

We are testing, thanks for reporting the problem. This is at http://usegalaxy.org, correct?

ADD REPLYlink written 2.5 years ago by Jennifer Hillman Jackson25k
1
gravatar for Jennifer Hillman Jackson
2.5 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hi Ana,

I was able to confirm this with an independent test. A ticket has been opened to track the correction. You can track that and testing after deployment to http://usegalaxy.org here:

MAF specific issue: https://github.com/galaxyproject/galaxy/issues/2187 Known issues: https://github.com/jennaj/support-known-issues/wiki

Thanks for reporting the problem! Jen, Galaxy team

ADD COMMENTlink written 2.5 years ago by Jennifer Hillman Jackson25k
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