Handling multiple PMOs pmotools-python

pmotools-runner.py combine_pmos

Can download multiple PMOs here

https://plasmogenepi.github.io/PMO_Docs/format/moz2018_PMO.json.gz

https://plasmogenepi.github.io/PMO_Docs/format/PathWeaverHeome1_PMO.json.gz

pmotools-runner.py combine_pmos --help

usage: pmotools-runner.py combine_pmos [-h] --pmo_files PMO_FILES --output
                                       OUTPUT [--overwrite]

options:
  -h, --help            show this help message and exit
  --pmo_files PMO_FILES
                        a list of PMO files to combine into 1 PMO file, must
                        be from same amplicon panel
  --output OUTPUT       Output new combined PMO file
  --overwrite           If output file exists, overwrite it

The list of PMO files can be given comma separated to thier relative paths from where you run the script or in a file where each line is a different file to combine

cd example 

wget https://plasmogenepi.github.io/PMO_Docs/format/moz2018_PMO.json.gz
wget https://plasmogenepi.github.io/PMO_Docs/format/PathWeaverHeome1_PMO.json.gz


pmotools-runner.py combine_pmos --pmo_files moz2018_PMO.json.gz,PathWeaverHeome1_PMO.json.gz --output combined_Heome1_PMO.json.gz --overwrite

The python code for combine_pmos script is below

pmotools-python/scripts/pmo_utils/combine_pmos.py

#!/usr/bin/env python3
import gzip
import os, argparse, json
from collections import defaultdict

import pandas as pd

from pmotools.pmo_utils.PMOWriter import PMOWriter
from pmotools.utils.small_utils import Utils
from pmotools.pmo_utils.PMOReader import PMOReader



def parse_args_combine_pmos():
    parser = argparse.ArgumentParser()
    parser.add_argument('--pmo_files', type=str, required=True, help='a list of PMO files to combine into 1 PMO file, must be from same amplicon panel')
    parser.add_argument('--output', type=str, required=True, help='Output new combined PMO file')
    parser.add_argument('--overwrite', action = 'store_true', help='If output file exists, overwrite it')

    return parser.parse_args()

def combine_pmos():
    args = parse_args_combine_pmos()

    # set up output
    args.output = PMOWriter.add_pmo_extension_as_needed(args.output, args.output.endswith(".gz"))
    Utils.outputfile_check(args.output, args.overwrite)

    # check if at least 2 PMO files supplied
    pmo_files_list = Utils.parse_delimited_input_or_file(args.pmo_files, ",")
    if len(pmo_files_list) < 2:
        raise Exception("Only supplied " + str(len(pmo_files_list)) + " but multiple PMO files were expected")

    # read in the PMOs
    pmos = PMOReader.read_in_pmos(pmo_files_list)

    # combine PMOs
    pmo_out = PMOReader.combine_multiple_pmos(pmos)

    # write
    PMOWriter.write_out_pmo(pmo_out, args.output, args.overwrite)


if __name__ == "__main__":
    combine_pmos()