NP-Omix / BioCompass

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Testing BioCompass 0.9.0 #44

Closed tiagolbiotech closed 7 years ago

tiagolbiotech commented 8 years ago

After uninstalling, updating, reinstalling and running BioCompass (0.9.0), I obtained the following error:

do BioCompass download-hits --outputdir /Users/Tiago/Desktop/dev/Cyanet/biocompass/ziemert_amycolatopsis/BioCompass/outputs/database_clusters $file; \
        done
Traceback (most recent call last):
  File "/Users/Tiago/anaconda2/bin/BioCompass", line 9, in <module>
    load_entry_point('BioCompass==0.9.0', 'console_scripts', 'BioCompass')()
  File "/Users/Tiago/anaconda2/lib/python2.7/site-packages/click-6.6-py2.7.egg/click/core.py", line 716, in __call__
    return self.main(*args, **kwargs)
  File "/Users/Tiago/anaconda2/lib/python2.7/site-packages/click-6.6-py2.7.egg/click/core.py", line 696, in main
    rv = self.invoke(ctx)
  File "/Users/Tiago/anaconda2/lib/python2.7/site-packages/click-6.6-py2.7.egg/click/core.py", line 1060, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/Users/Tiago/anaconda2/lib/python2.7/site-packages/click-6.6-py2.7.egg/click/core.py", line 889, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/Users/Tiago/anaconda2/lib/python2.7/site-packages/click-6.6-py2.7.egg/click/core.py", line 534, in invoke
    return callback(*args, **kwargs)
  File "/Users/Tiago/anaconda2/lib/python2.7/site-packages/BioCompass-0.9.0-py2.7.egg/BioCompass/cli.py", line 19, in downloadHits
    download_hits(mgbfile, outputdir)
  File "/Users/Tiago/anaconda2/lib/python2.7/site-packages/BioCompass-0.9.0-py2.7.egg/BioCompass/BioCompass.py", line 234, in download_hits
    c = antiSMASH_file(filename)
  File "/Users/Tiago/anaconda2/lib/python2.7/site-packages/BioCompass-0.9.0-py2.7.egg/BioCompass/BioCompass.py", line 183, in __init__
    self.load(filename)
  File "/Users/Tiago/anaconda2/lib/python2.7/site-packages/BioCompass-0.9.0-py2.7.egg/BioCompass/BioCompass.py", line 194, in load
    parsed = parse_antiSMASH(f.read())
  File "/Users/Tiago/anaconda2/lib/python2.7/site-packages/BioCompass-0.9.0-py2.7.egg/BioCompass/BioCompass.py", line 97, in parse_antiSMASH
    parsed = re.search(rule, content, re.VERBOSE).groupdict()
AttributeError: 'NoneType' object has no attribute 'groupdict'