LobSTR_pipeline.py

import os
import sys
from LobSTR_to_csv import process_files


def analysis_pipeline(in_d, out_d):
    """Runs an analysis while looping over a given directory.

    :param in_d: str - path to the directory with the BAM files that need to be analysed.
    :param out_d: str - path to the output directory.
    """
    for filename in os.listdir(in_d):
        if filename.endswith(".bam"):
            prefix = out_d + filename.split("/")[-1].replace(".bam", "")
            singularity_mount_path = "/hpc/diaggen:/hpc/diaggen"
            singularity_img = "/hpc/diaggen/software/singularity_cache/lobster_v4.0.0.img"
            lobstr_command = f"allelotype --command classify --bam {in_d}{filename} --noise_model " \
                             f"/hpc/diaggen/users/Gabe/tools/lobSTR/models/illumina_v3.pcrfree --strinfo " \
                             f"/hpc/diaggen/users/Gabe/tools/lobSTR/lobstr_new/lobstr_v3.0.2_hg19_strinfo.tab " \
                             f"--index-prefix " \
                             f"/hpc/diaggen/users/Gabe/tools/lobSTR/lobstr_new/lobstr_hg19_ref/lobSTR_ " \
                             f"--out {prefix}"

            action = f"singularity exec -B {singularity_mount_path} {singularity_img} {lobstr_command}"
            os.system(action)


if __name__ == "__main__":
    print("Staring analysis pipeline...")
    analysis_pipeline(sys.argv[1], sys.argv[2])
    print("Analysis complete.")
    print("Processing output now...")
    process_files(sys.argv[2])
    print("Processing complete.")