MafAnnotator.py

#!/usr/bin/env python

import sys
import argparse
import logging

from AnnotatorCore import setsampleidsfileterfile
from AnnotatorCore import setcancerhotspotsbaseurl
from AnnotatorCore import setoncokbbaseurl
from AnnotatorCore import setoncokbapitoken
from AnnotatorCore import readCancerTypes
from AnnotatorCore import validate_oncokb_token
from AnnotatorCore import processalterationevents
from AnnotatorCore import QueryType
from AnnotatorCore import ReferenceGenome

logging.basicConfig(level=logging.INFO)
log = logging.getLogger('MafAnnotator')


def main(argv):
    if argv.help:
        log.info(
            '\n'
            'MafAnnotator.py -i <input MAF file> -o <output MAF file> [-p previous results] [-c <input clinical file>] '
            '[-s sample list filter] [-t <default tumor type>] [-u oncokb-base-url] [-b oncokb api bear token] [-a] '
            '[-q query type] [-r default reference genome] [-d include descriptions]\n'
            'For definitions of the MAF format, please see https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format/\n\n'
            'Essential MAF columns for querying HGVSp_Short and HGVSp(case insensitive):\n'
            '    Hugo_Symbol: Hugo gene symbol\n'
            '    Tumor_Sample_Barcode: sample ID\n'
            '    HGVSp(query type: HGVSp): protein change in HGVSp format\n'
            '    HGVSp_Short(query type: HGVSp_Short): protein change in HGVSp format using 1-letter amino-acid codes\n'
            'Essential MAF columns for querying HGVSg(case insensitive):\n'
            '    Tumor_Sample_Barcode: sample ID\n'
            '    HGVSg: Genomic change in HGVSg format\n'
            'Essential MAF columns for querying HGVSc(case insensitive):\n'
            '    Tumor_Sample_Barcode: sample ID\n'
            '    HGVSc: cDNA change in HGVSc format\n'
            'Recommended column for mixed somatic/germline annotation:\n'
            '    Mutation_Status: row mutation status. Germline rows use germline endpoints, all other values default to somatic.\n'
            'Essential MAF columns for querying genomic change(case insensitive):\n'
            '    Tumor_Sample_Barcode: sample ID\n'
            '    Chromosome: Chromosome number\n'
            '    Start_Position: Mutation start coordinate\n'
            '    End_Position: Mutation end coordinate\n'
            '    Reference_Allele: The plus strand reference allele at this position\n'
            '    Tumor_Seq_Allele1: Primary data genotype for tumor sequencing (discovery) allele\n'
            '    Tumor_Seq_Allele2: Tumor sequencing (discovery) allele 2\n'
            'Essential clinical columns:\n'
            '    SAMPLE_ID: sample ID\n'
            '    ONCOTREE_CODE: tumor type code from oncotree (http://oncotree.mskcc.org)\n'
            'Cancer type will be assigned based on the following priority:\n'
            '    1) ONCOTREE_CODE in clinical data file\n'
            '    2) ONCOTREE_CODE exist in MAF\n'
            '    3) default tumor type (-t)\n'
            'Query type only allows the following values (case-insensitive):\n'
            '    - HGVSp_Short\n'
            '      It reads from column HGVSp_Short or Alteration\n'
            '    - HGVSp\n'
            '      It reads from column HGVSp or Alteration\n'
            '    - HGVSg\n'
            '      It reads from column HGVSg or Alteration\n'
            '    - HGVSc\n'
            '      It reads from column HGVSc or Alteration\n'
            '    - Genomic_Change\n'
            '      It reads from columns Chromosome, Start_Position, End_Position, Reference_Allele, Tumor_Seq_Allele1 and Tumor_Seq_Allele2  \n'
            'The annotator infers row mutation status from Mutation_Status and defaults unknown values to somatic.\n'
            'Germline supports HGVSc, HGVSg, or Genomic_Change query types.\n'
            'Somatic supports HGVSp_Short, HGVSp, HGVSg, or Genomic_Change query types.\n'
            'Reference Genome only allows the following values(case-insensitive):\n'
            '    - GRCh37\n'
            '      GRCh38\n'
            'Default OncoKB base url is https://www.oncokb.org.\n'
        )
        sys.exit()
    if argv.input_file == '' or argv.output_file == '' or argv.oncokb_api_bearer_token == '':
        required_params = []
        if argv.input_file == '':
            required_params.append('-i')
        if argv.output_file == '':
            required_params.append('-o')
        if argv.oncokb_api_bearer_token == '':
            required_params.append('-b')

        log.error('The parameter(s) ' + ', '.join(required_params) + ' can not be empty')
        log.info('For help: python MafAnnotator.py -h')
        sys.exit(2)

    if argv.sample_ids_filter:
        setsampleidsfileterfile(argv.sample_ids_filter)
    if argv.cancer_hotspots_base_url:
        setcancerhotspotsbaseurl(argv.cancer_hotspots_base_url)
    if argv.oncokb_api_url:
        setoncokbbaseurl(argv.oncokb_api_url)
    setoncokbapitoken(argv.oncokb_api_bearer_token)

    cancertypemap = {}
    if argv.input_clinical_file:
        readCancerTypes(argv.input_clinical_file, cancertypemap)

    log.info('annotating %s ...' % argv.input_file)

    user_input_query_type = None
    if argv.query_type is not None:
        try:
            user_input_query_type = QueryType[argv.query_type.upper()]
        except KeyError:
            log.error(
                'Query type is not acceptable. Only the following allows(case insensitive): HGVSp_Short, HGVSp, HGVSg, HGVSc (germline only), Genomic_Change')
            raise

    default_reference_genome = None
    if argv.default_reference_genome is not None:
        try:
            default_reference_genome = ReferenceGenome[argv.default_reference_genome.upper()]
        except KeyError:
            log.error(
                'Reference genome is not acceptable. Only the following allows(case insensitive): GRCh37, GRCh38')
            raise

    validate_oncokb_token()

    processalterationevents(argv.input_file, argv.output_file, argv.previous_result_file, argv.default_cancer_type,
                            cancertypemap, argv.annotate_hotspots, user_input_query_type, default_reference_genome,
                            argv.include_descriptions)

    log.info('done!')


if __name__ == "__main__":
    parser = argparse.ArgumentParser(add_help=False)
    parser.add_argument('-h', dest='help', action="store_true", default=False)
    parser.add_argument('-i', dest='input_file', default='', type=str)
    parser.add_argument('-o', dest='output_file', default='', type=str)
    parser.add_argument('-p', dest='previous_result_file', default='', type=str)
    parser.add_argument('-c', dest='input_clinical_file', default='', type=str)
    parser.add_argument('-s', dest='sample_ids_filter', default='', type=str)
    parser.add_argument('-t', dest='default_cancer_type', default='', type=str)
    parser.add_argument('-u', dest='oncokb_api_url', default='', type=str)
    parser.add_argument('-a', dest='annotate_hotspots', action="store_true", default=False)
    parser.add_argument('-v', dest='cancer_hotspots_base_url', default='', type=str)
    parser.add_argument('-b', dest='oncokb_api_bearer_token', default='', type=str)
    parser.add_argument('-q', dest='query_type', default=None, type=str)
    parser.add_argument('-r', dest='default_reference_genome', default=None, type=str)
    parser.add_argument('-d', dest='include_descriptions', action="store_true", default=False)
    parser.set_defaults(func=main)

    args = parser.parse_args()
    args.func(args)