run_pipeline_variant_calling.py

import variant_calling
import os, shutil
import variant_annotation


def call_variant_caller(working_directory, tumor_bam, germline_bam, var_maptype, var_variantcaller, threads_p,
                        s_name, tumor_only, tumor_interval=None, germline_interval=None, to_temp=[False, None]):

    if to_temp[0]:
        os.makedirs(os.path.dirname(to_temp[1]), exist_ok=True)
        shutil.copy(working_directory, to_temp[1])
        wd = to_temp[1]
    else:
        wd = working_directory

    if wd[-1] == "/" or wd[-1] == "\\":
        wd = wd[:-1]

    gm = germline_bam

    if gm[-1] == "/" or gm[-1] == "\\":
        gm = gm[:-1]

    gm_interval = germline_interval

    if gm[-1] == "/" or gm[-1] == "\\":
        gm = gm[:-1]

    if var_variantcaller == "Mutect2" or var_variantcaller == "Mutect2_gatk3":
        pipeline2 = variant_calling.VariantCall(variant_caller=var_variantcaller, thrds=threads_p, map_type=var_maptype,
                                                germline_bam=gm, germline_interval=gm_interval, wd=wd,
                                                tumor_bam=tumor_bam, tumor_interval=tumor_interval,
                                                sample_name=s_name, tumor_only=tumor_only)
    else:
        pipeline2 = variant_calling.VariantCall(variant_caller=var_variantcaller, thrds=threads_p, map_type=var_maptype,
                                                germline_bam=gm, germline_interval=None, wd=wd, tumor_bam=tumor_bam,
                                                tumor_interval=None, sample_name=s_name,  tumor_only=tumor_only)
    pipeline2_success = pipeline2.run_pipeline()

    # annotate = variant_annotation.VariantAnnotation(variant_annotater="Annovar", thread_v=threads_p, wd=pipeline2_success, sample_name=s_name, will_annotate=[], annotate_all=True)
    #
    # annotate.run_annotation()

    return pipeline2_success


# call_variant_caller(var_variantcaller="Mutect2", threads_p=3, var_maptype="Bwa",
#                     germline_bam="/home/bioinformaticslab/Desktop/AMBRY/DUYGU/Sample_40/Bwa/PreProcess/GATK4_MDUP_Bwa_40_MergedBAM.bam",
#                     working_directory="/home/bioinformaticslab/Desktop/AMBRY/DUYGU/Sample_37",
#                     tumor_bam="GATK4_MDUP_Bwa_37_MergedBAM.bam", s_name="S37", tumor_only="No")