bioflow.pre_processing package


bioflow.pre_processing.remap_IDs module

Remaps the IDs of the gene identifiers to a different organism before processing them

These are mainly interesting to for the applications where there is little information about the genetic networks specific to the organism in question and we would like to use it as a model for another organism (eg mice vs human) and we want to project genes associated to the phenotype in the model organism into the networks associated to the original organism.

bioflow.pre_processing.remap_IDs.translate_identifiers(data_source_location, data_dump_location, translation_file_location, gene_to_id_file_location)[source]

Performs a translation of gene identifiers from one organism to another one.

  • data_source_location – where the gene id to translate are
  • data_dump_location – where the translated gene ids will be stored
  • translation_file_location – where the file that contains gene id mappings is located. expects a .tsv file with [Source org gene id, dest org gene id, dest org gene symbol, confidence (1=high, 0=low), …] per line
  • gene_to_id_file_location – (optional) where the file that maps gene ids to HGCN names expects a .tsv file with [Gene stable ID, Transcript stable ID, Gene name, HGNC symbol]

bioflow.pre_processing.rna_counts_analysis module

Module contents