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pinellolab / haystack_bio

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

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code organization

rfarouni opened this issue · comments

commented
  1. These files in root are not needed
  • haystack_download_genome.py
  • haystack_hotspots.py
  • haystack_motifs.py
  • haystack_pipeline.py

  1. Do we need all the files in haystack_data/extra ?

  2. The three files below contain functions used by all the modules. Can they be combined under a single file? Are all the functions needed by the modules?

  • bioutilities.py
  • external.py
  • haystack_common.py
  1. The module names are not all-lowercase. haystack in the beginning is not descriptive of what the module does.
  • haystack_download_genome_CORE.py
  • haystack_hotspots_CORE.py
  • haystack_motifs_CORE.py
  • haystack_pipeline_CORE.py
  • haystack_tf_activity_plane_CORE.py

PEP8: Modules should have short, all-lowercase names. Underscores can be used in the module name if it improves readability. Python packages should also have short, all-lowercase names, although the use of underscores is discouraged.