PICASO.load_utils
=================

.. py:module:: PICASO.load_utils


Functions
---------

.. autoapisummary::

   PICASO.load_utils.download_and_unzip
   PICASO.load_utils.load_go
   PICASO.load_utils.load_uniprot_location
   PICASO.load_utils.load_omnipath
   PICASO.load_utils.load_STRING
   PICASO.load_utils.load_opentargets
   PICASO.load_utils.load_reactome
   PICASO.load_utils.load_npinter
   PICASO.load_utils.load_kegg
   PICASO.load_utils.load_human_transcription_factors


Module Contents
---------------

.. py:function:: download_and_unzip(download_url_link, dir_path, zipped_filename, destination_dir_name, unzip=True, force_zip=False, force_gz=False)

.. py:function:: load_go(kg: networkx.DiGraph, data_dir, source='GeneOntology', interaction_harmonize={'NOT': 'relevant_in', 'acts_upstream_of': 'relevant_in', 'acts_upstream_of_negative_effect': 'relevant_in', 'acts_upstream_of_or_within': 'relevant_in', 'acts_upstream_of_or_within_negative_effect': 'relevant_in', 'acts_upstream_of_or_within_positive_effect': 'relevant_in', 'acts_upstream_of_positive_effect': 'relevant_in', 'colocalizes_with': 'relevant_in', 'contributes_to': 'activates', 'enables': 'activates', 'involved_in': 'relevant_in', 'is_active_in': 'activates', 'located_in': 'relevant_in', 'part_of': 'relevant_in'})

.. py:function:: load_uniprot_location(kg: networkx.DiGraph, data_dir, source='uniprot_celloc')

.. py:function:: load_omnipath(kg: networkx.DiGraph, data_dir, source='omnipath')

.. py:function:: load_STRING(kg: networkx.DiGraph, data_dir, mart_file='oct2014_mart_export.txt', source='STRING', use_evidences=['fusion', 'coexpression', 'experiments', 'database', 'textmining'])

.. py:function:: load_opentargets(kg: networkx.DiGraph, data_dir, source='opentargets', min_disease_association_score=0.8)

.. py:function:: load_reactome(kg: networkx.DiGraph, data_dir, source='reactome')

.. py:function:: load_npinter(kg: networkx.DiGraph, data_dir, source='npinter5')

.. py:function:: load_kegg(kg: networkx.DiGraph, data_dir, source='kegg', hallmark_genesets='kegg_gmts/human/h.all.v2023.2.Hs.symbols.gmt', curated_genesets='kegg_gmts/human/c2.all.v2023.2.Hs.symbols.gmt', load_reactome=False, load_wp=True)

.. py:function:: load_human_transcription_factors(kg: networkx.DiGraph, data_dir, source='human_transcription_factors')