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nboley / grit

GNU General Public License v3.0
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fix call to determine_read_strand_params in PolyAReads #3

Open boegel opened 8 years ago

boegel commented 8 years ago

This fixes the following crash with GRIT 2.0.5:

Traceback (most recent call last):
  File "/apps/gent/SL6/sandybridge/software/GRIT/2.0.5-intel-2016b-Python-2.7.12/bin/run_grit", line 4, in <module>
    __import__('pkg_resources').run_script('GRIT==2.0.5', 'run_grit')
  File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 719, in run_script
  File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 1511, in run_script
  File "/apps/gent/SL6/sandybridge/software/GRIT/2.0.5-intel-2016b-Python-2.7.12/lib/python2.7/site-packages/GRIT-2.0.5-py2.7-linux-x86_64.egg/EGG-INFO/scripts/run_grit", line 884, in <module>

  File "/apps/gent/SL6/sandybridge/software/GRIT/2.0.5-intel-2016b-Python-2.7.12/lib/python2.7/site-packages/GRIT-2.0.5-py2.7-linux-x86_64.egg/EGG-INFO/scripts/run_grit", line 777, in main

  File "/apps/gent/SL6/sandybridge/software/GRIT/2.0.5-intel-2016b-Python-2.7.12/lib/python2.7/site-packages/GRIT-2.0.5-py2.7-linux-x86_64.egg/EGG-INFO/scripts/run_grit", line 735, in iteritems

  File "/apps/gent/SL6/sandybridge/software/GRIT/2.0.5-intel-2016b-Python-2.7.12/lib/python2.7/site-packages/GRIT-2.0.5-py2.7-linux-x86_64.egg/EGG-INFO/scripts/run_grit", line 683, in _build_elements

  File "/apps/gent/SL6/sandybridge/software/GRIT/2.0.5-intel-2016b-Python-2.7.12/lib/python2.7/site-packages/GRIT-2.0.5-py2.7-linux-x86_64.egg/EGG-INFO/scripts/run_grit", line 364, in get_reads

  File "/apps/gent/SL6/sandybridge/software/GRIT/2.0.5-intel-2016b-Python-2.7.12/lib/python2.7/site-packages/GRIT-2.0.5-py2.7-linux-x86_64.egg/EGG-INFO/scripts/run_grit", line 351, in _load_polya_reads

  File "build/bdist.linux-x86_64/egg/grit/files/reads.py", line 960, in init
AttributeError: type object 'Reads' has no attribute 'determine_read_strand_param'