code package

Subpackages

• code.pipeline package
  • Submodules
  • code.pipeline.clean_input module
  • code.pipeline.make_aggregate module
  • code.pipeline.mixed2gaf module
  • code.pipeline.run_argot2 module
  • code.pipeline.run_iprs module
  • code.pipeline.run_mm_preproc module
  • code.pipeline.run_pannzer module
  • code.pipeline.run_rbh_blast module
  • Module contents
• code.process package
  • Submodules
  • code.process.clean_tair module
  • code.process.clean_uniprot module
  • Module contents
• code.utils package
  • Submodules
  • code.utils.basic_utils module
  • code.utils.blast_utils module
  • code.utils.get_longest_transcript module
  • code.utils.split_fa module
  • Module contents

Submodules

code.gomap_aggregate module

This file includes the steps to aggregate

code.gomap_aggregate.aggregate(config)

code.gomap_preprocess module

Importing all the modules necessary for running the pipeline pprint is only needed for debugging purposes

code.gomap_preprocess.run_preprocess(config)

A really useful function.

Returns None

code.gomap_setup module

This submodule lets the user download the data files necessary for running the GOMAP pipline from CyVerse

Currently the files are stored in Gokul’s personal directory so the download has to be initiated by gokul’s own CyVerse account with icommands

code.gomap_setup.setup(config)

Module contents