metadata_processing module¶

This script serves to process metadata from TCGA, ICGC, SRA and outputs a standardized table Metadata Table [sample_id, case_id, condition, bio_project]

usage: python metadata_processing.py -i <path-to-fileEndpt-json> … -s <path-to-csv-files> -t <path-to-json> -t <path-to-json> … -o <outpath.csv>

metadata_processing.parse_icgc_json_files(files)[source]¶

Read json files from list and extract relevant values

Parameters: files – as list
Returns: icgc_metadata: dict

metadata_processing.parse_tcga_json_files(files)[source]¶

Read json files from list and extract relevant values

Parameters: files – as list
Returns: tcga_metadata: dict