old_contents: #!/usr/bin/env python
  """ Setup script for the gwide package."""
  
  __author__ = 'Tomasz W. Turowski'
  
  from setuptools import setup, find_packages
  
  
  setup(
      name='gwide',
      version='0.3.5',
      # py_modules=['gwide'],
      packages=find_packages(),
      install_requires=[
          'pypeaks',
          'pandas',
          'ruffus',
          'PyYAML',
          'matplotlib',
          'numpy'
      ],
      entry_points='''
          [console_scripts]
          gwidetRNA=gwide.gwidetRNA:tRNA
          gwideHittable=gwide.gwideHittable:hittable
          gwidePlot=gwide.gwidePlot:plot
          getFastaSeqs=gwide.parserTools:getFastaSeqs
          getGeneLength=gwide.parserTools:getGeneLength
          getIdFromName=gwide.parserTools:getIdFromName
          getNameFromId=gwide.parserTools:getNameFromId
          getGeneNamesFromGTF=gwide.parserTools:getGeneNamesFromGTF
      ''',
      scripts=[
          'gwide/scripts/novo2concat.py',
          'gwide/scripts/defineTerminator.py',
          'gwide/scripts/geneUsage.py'
      ]
      author="Tomasz W. Turowski",
      description='Set of tools to downstream analysis of pyCRAC data',
      long_description='',
      author_email="twturowski@gmail.com",
      classifiers=[
              'Development Status :: 2 - Pre-Alpha',
              'Intended Audience :: Science/Research',
              'License :: OSI Approved :: Apache',
              'Topic :: Scientific/Engineering :: Bio-Informatics']
  )
  
new_contents: #!/usr/bin/env python
  """ Setup script for the gwide package."""
  
  __author__ = 'Tomasz W. Turowski'
  
  from setuptools import setup, find_packages
  
  
  setup(
      name='gwide',
      version='0.3.5',
      # py_modules=['gwide'],
      packages=find_packages(),
      install_requires=[
          'pypeaks',
          'pandas',
          'ruffus',
          'PyYAML',
          'matplotlib',
          'numpy'
      ],
      entry_points='''
          [console_scripts]
          gwidetRNA=gwide.gwidetRNA:tRNA
          gwideHittable=gwide.gwideHittable:hittable
          gwidePlot=gwide.gwidePlot:plot
          getFastaSeqs=gwide.parserTools:getFastaSeqs
          getGeneLength=gwide.parserTools:getGeneLength
          getIdFromName=gwide.parserTools:getIdFromName
          getNameFromId=gwide.parserTools:getNameFromId
          getGeneNamesFromGTF=gwide.parserTools:getGeneNamesFromGTF
      ''',
      scripts=[
          'gwide/scripts/novo2concat.py',
          'gwide/scripts/defineTerminator.py',
          'gwide/scripts/geneUsage.py'
      ],
      author="Tomasz W. Turowski",
      description='Set of tools to downstream analysis of pyCRAC data',
      long_description='',
      author_email="twturowski@gmail.com",
      classifiers=[
              'Development Status :: 2 - Pre-Alpha',
              'Intended Audience :: Science/Research',
              'License :: OSI Approved :: Apache',
              'Topic :: Scientific/Engineering :: Bio-Informatics']
  )
  
subject: package files ordered