import argparse
import subprocess
import json
import os
import textwrap
import random as rm
import datetime
import pysam
import random as r
import regex as re
import pipeline as pipeline
import functions as f


if __name__ == '__main__':

	parser = argparse.ArgumentParser('This is the Coolest Pipeline you have ever seen')
	parser.add_argument('-v', '--version', action='version', version='Powercall v3.2.0')

	parser.add_argument('-c', '--cfg', help="Configuration file in json format")
	parser.add_argument('-s', '--samplesheet', help="Samplesheet that contains filepaths and samples associated", required=True)
	parser.add_argument('-d', '--design', help="Design of the NGS experiment [Enrichment,Amplicon].",choices=['Enrichment','Amplicon'])
	parser.add_argument('-p', '--panel', help="Type of Panel used for the analysis [TrusightCardio (illumina), TrusightCancer (illumina), TrusightOne (illumina), BRCAMASTRDx (MULTIPLICOM), ALPORTMASTR (MULTIPLICOM), HTC (SophiaGenetics), CustomSSQXT (Custom SureSelect QXT Agilent), CustomHPHS (Custom HaloPlex HS Agilent), Custom (Other Custom panel), CCP17]",
		choices="[TrusightCardio, TrusightCancer, TrusightOne, BRCAMASTRDx, ALPORTMASTR, HCS, CustomSSQXT, CustomHPHS, Custom, CCP17]")
	parser.add_argument('-a', '--analysis', help="Type of analysis [Germline (Multisample), GermlineSS (Singlesample), SomaticCC (Case-Control), Somatic (only Case)].", choices=['Germline', 'GermlineSS','SomaticCC','Somatic'], default='Germline')
	parser.add_argument('-id','--run_id', help="Run id [YYYYMMDD_Run_NRUN_PANEL}", required=True)
	parser.add_argument('-w', '--workdir', help="Working Directory. Use this option if you want to work in a precise directory. Default: '/home/run_id'", default=None)
	parser.add_argument('--workflow', help="String that indicates which steps the analysis must do: A-> Alignment, R-> AddOrReplaceReadGroups, M-> MarkDuplicates, I-> IndelRealigner, B-> BaseRecalibrator, V-> Variant Calling, F-> Features Extraction, E-> Annotation. Es: --start AMIBVFE indicates all steps (like --start ALL), --start MIBV starts from MarkDuplicates and ends to Variant Calling. Default: ALL ", default='ALL')
	parser.add_argument('-BP', '--GATKBestPractices', help="GATK Best practices workflow", action='store_true')

	start_time = datetime.datetime.now()
	success = subprocess.call('clear')
	
	global opts
	opts = parser.parse_args()

	dirs=dict()
	
	if opts.cfg != None:
		cfg = json.loads((open(opts.cfg).read()).encode('utf8'))
	else:
		cfg = json.loads((open('/'.join(os.path.dirname(os.path.abspath(__file__)).split('/')[:-1]) + '/configs/Powercall.default.cfg.json').read()).encode('utf8'))
	
	if opts.workdir != None:
		work_dir = opts.workdir
	else:
		work_dir = opts.run_id

	dirs = f.init_dirs(work_dir,opts)
	f.makedirs([work_dir, work_dir+'/STORAGE', work_dir+'/OUTPUT', dirs['storage'], dirs['out'], dirs['delete'], dirs['log'], ])

	design,target_list,target_bed,transcripts_list,cnv_target_list,cnv_target_bed,cnv_ref_ploidy,cnv_ref_calls = f.panel_check(opts.panel,cfg)

	if opts.design != None:
		design = opts.design

	workflow = opts.workflow
	if workflow == 'ALL':
		workflow = 'ARMIBVFEC'

	if design == 'Amplicon':
		workflow=re.sub('MIB','',workflow)
		workflow=re.sub('M','',workflow)

	if opts.GATKBestPractices:
		workflow=re.sub('I','',workflow)

	if opts.analysis == 'Germline':
		pipeline.Pipeline_Germline_Multisample(workflow,opts.samplesheet,design,opts.panel,dirs,cfg,opts,target_list,target_bed,transcripts_list,cnv_target_list,cnv_target_bed,cnv_ref_ploidy,cnv_ref_calls)

	if opts.analysis == 'GermlineSS':
		pipeline.Pipeline_Germline_Singlesample(workflow,opts.samplesheet,design,opts.panel,dirs,cfg,opts,target_list,target_bed,transcripts_list,cnv_target_list,cnv_target_bed,cnv_ref_ploidy,cnv_ref_calls)

	elif opts.analysis == 'SomaticCC':
		pipeline.Pipeline_Somatic_Case_Control(workflow,opts.samplesheet,design,opts.panel,dirs,cfg,opts,target_list,target_bed,transcripts_list,cnv_target_list,cnv_target_bed,cnv_ref_ploidy,cnv_ref_calls)

	elif opts.analysis == 'Somatic':
		pipeline.Pipeline_Somatic(workflow,opts.samplesheet,design,opts.panel,dirs,cfg,opts,target_list,target_bed,transcripts_list,cnv_target_list,cnv_target_bed,cnv_ref_ploidy,cnv_ref_calls)

	elapsed_time = divmod((datetime.datetime.now() - start_time).total_seconds(),60)
	print("\nTime elapsed: %d min, %d sec" % elapsed_time)

86477f624ba98eaa48add67e4a567bea7755515b
<mask token>

<mask token>
if __name__ == '__main__':
    parser = argparse.ArgumentParser(
        'This is the Coolest Pipeline you have ever seen')
    parser.add_argument('-v', '--version', action='version', version=
        'Powercall v3.2.0')
    parser.add_argument('-c', '--cfg', help='Configuration file in json format'
        )
    parser.add_argument('-s', '--samplesheet', help=
        'Samplesheet that contains filepaths and samples associated',
        required=True)
    parser.add_argument('-d', '--design', help=
        'Design of the NGS experiment [Enrichment,Amplicon].', choices=[
        'Enrichment', 'Amplicon'])
    parser.add_argument('-p', '--panel', help=
        'Type of Panel used for the analysis [TrusightCardio (illumina), TrusightCancer (illumina), TrusightOne (illumina), BRCAMASTRDx (MULTIPLICOM), ALPORTMASTR (MULTIPLICOM), HTC (SophiaGenetics), CustomSSQXT (Custom SureSelect QXT Agilent), CustomHPHS (Custom HaloPlex HS Agilent), Custom (Other Custom panel), CCP17]'
        , choices=
        '[TrusightCardio, TrusightCancer, TrusightOne, BRCAMASTRDx, ALPORTMASTR, HCS, CustomSSQXT, CustomHPHS, Custom, CCP17]'
        )
    parser.add_argument('-a', '--analysis', help=
        'Type of analysis [Germline (Multisample), GermlineSS (Singlesample), SomaticCC (Case-Control), Somatic (only Case)].'
        , choices=['Germline', 'GermlineSS', 'SomaticCC', 'Somatic'],
        default='Germline')
    parser.add_argument('-id', '--run_id', help=
        'Run id [YYYYMMDD_Run_NRUN_PANEL}', required=True)
    parser.add_argument('-w', '--workdir', help=
        "Working Directory. Use this option if you want to work in a precise directory. Default: '/home/run_id'"
        , default=None)
    parser.add_argument('--workflow', help=
        'String that indicates which steps the analysis must do: A-> Alignment, R-> AddOrReplaceReadGroups, M-> MarkDuplicates, I-> IndelRealigner, B-> BaseRecalibrator, V-> Variant Calling, F-> Features Extraction, E-> Annotation. Es: --start AMIBVFE indicates all steps (like --start ALL), --start MIBV starts from MarkDuplicates and ends to Variant Calling. Default: ALL '
        , default='ALL')
    parser.add_argument('-BP', '--GATKBestPractices', help=
        'GATK Best practices workflow', action='store_true')
    start_time = datetime.datetime.now()
    success = subprocess.call('clear')
    global opts
    opts = parser.parse_args()
    dirs = dict()
    if opts.cfg != None:
        cfg = json.loads(open(opts.cfg).read().encode('utf8'))
    else:
        cfg = json.loads(open('/'.join(os.path.dirname(os.path.abspath(
            __file__)).split('/')[:-1]) +
            '/configs/Powercall.default.cfg.json').read().encode('utf8'))
    if opts.workdir != None:
        work_dir = opts.workdir
    else:
        work_dir = opts.run_id
    dirs = f.init_dirs(work_dir, opts)
    f.makedirs([work_dir, work_dir + '/STORAGE', work_dir + '/OUTPUT', dirs
        ['storage'], dirs['out'], dirs['delete'], dirs['log']])
    (design, target_list, target_bed, transcripts_list, cnv_target_list,
        cnv_target_bed, cnv_ref_ploidy, cnv_ref_calls) = f.panel_check(opts
        .panel, cfg)
    if opts.design != None:
        design = opts.design
    workflow = opts.workflow
    if workflow == 'ALL':
        workflow = 'ARMIBVFEC'
    if design == 'Amplicon':
        workflow = re.sub('MIB', '', workflow)
        workflow = re.sub('M', '', workflow)
    if opts.GATKBestPractices:
        workflow = re.sub('I', '', workflow)
    if opts.analysis == 'Germline':
        pipeline.Pipeline_Germline_Multisample(workflow, opts.samplesheet,
            design, opts.panel, dirs, cfg, opts, target_list, target_bed,
            transcripts_list, cnv_target_list, cnv_target_bed,
            cnv_ref_ploidy, cnv_ref_calls)
    if opts.analysis == 'GermlineSS':
        pipeline.Pipeline_Germline_Singlesample(workflow, opts.samplesheet,
            design, opts.panel, dirs, cfg, opts, target_list, target_bed,
            transcripts_list, cnv_target_list, cnv_target_bed,
            cnv_ref_ploidy, cnv_ref_calls)
    elif opts.analysis == 'SomaticCC':
        pipeline.Pipeline_Somatic_Case_Control(workflow, opts.samplesheet,
            design, opts.panel, dirs, cfg, opts, target_list, target_bed,
            transcripts_list, cnv_target_list, cnv_target_bed,
            cnv_ref_ploidy, cnv_ref_calls)
    elif opts.analysis == 'Somatic':
        pipeline.Pipeline_Somatic(workflow, opts.samplesheet, design, opts.
            panel, dirs, cfg, opts, target_list, target_bed,
            transcripts_list, cnv_target_list, cnv_target_bed,
            cnv_ref_ploidy, cnv_ref_calls)
    elapsed_time = divmod((datetime.datetime.now() - start_time).
        total_seconds(), 60)
    print('\nTime elapsed: %d min, %d sec' % elapsed_time)

import argparse
import subprocess
import json
import os
import textwrap
import random as rm
import datetime
import pysam
import random as r
import regex as re
import pipeline as pipeline
import functions as f
if __name__ == '__main__':
    parser = argparse.ArgumentParser(
        'This is the Coolest Pipeline you have ever seen')
    parser.add_argument('-v', '--version', action='version', version=
        'Powercall v3.2.0')
    parser.add_argument('-c', '--cfg', help='Configuration file in json format'
        )
    parser.add_argument('-s', '--samplesheet', help=
        'Samplesheet that contains filepaths and samples associated',
        required=True)
    parser.add_argument('-d', '--design', help=
        'Design of the NGS experiment [Enrichment,Amplicon].', choices=[
        'Enrichment', 'Amplicon'])
    parser.add_argument('-p', '--panel', help=
        'Type of Panel used for the analysis [TrusightCardio (illumina), TrusightCancer (illumina), TrusightOne (illumina), BRCAMASTRDx (MULTIPLICOM), ALPORTMASTR (MULTIPLICOM), HTC (SophiaGenetics), CustomSSQXT (Custom SureSelect QXT Agilent), CustomHPHS (Custom HaloPlex HS Agilent), Custom (Other Custom panel), CCP17]'
        , choices=
        '[TrusightCardio, TrusightCancer, TrusightOne, BRCAMASTRDx, ALPORTMASTR, HCS, CustomSSQXT, CustomHPHS, Custom, CCP17]'
        )
    parser.add_argument('-a', '--analysis', help=
        'Type of analysis [Germline (Multisample), GermlineSS (Singlesample), SomaticCC (Case-Control), Somatic (only Case)].'
        , choices=['Germline', 'GermlineSS', 'SomaticCC', 'Somatic'],
        default='Germline')
    parser.add_argument('-id', '--run_id', help=
        'Run id [YYYYMMDD_Run_NRUN_PANEL}', required=True)
    parser.add_argument('-w', '--workdir', help=
        "Working Directory. Use this option if you want to work in a precise directory. Default: '/home/run_id'"
        , default=None)
    parser.add_argument('--workflow', help=
        'String that indicates which steps the analysis must do: A-> Alignment, R-> AddOrReplaceReadGroups, M-> MarkDuplicates, I-> IndelRealigner, B-> BaseRecalibrator, V-> Variant Calling, F-> Features Extraction, E-> Annotation. Es: --start AMIBVFE indicates all steps (like --start ALL), --start MIBV starts from MarkDuplicates and ends to Variant Calling. Default: ALL '
        , default='ALL')
    parser.add_argument('-BP', '--GATKBestPractices', help=
        'GATK Best practices workflow', action='store_true')
    start_time = datetime.datetime.now()
    success = subprocess.call('clear')
    global opts
    opts = parser.parse_args()
    dirs = dict()
    if opts.cfg != None:
        cfg = json.loads(open(opts.cfg).read().encode('utf8'))
    else:
        cfg = json.loads(open('/'.join(os.path.dirname(os.path.abspath(
            __file__)).split('/')[:-1]) +
            '/configs/Powercall.default.cfg.json').read().encode('utf8'))
    if opts.workdir != None:
        work_dir = opts.workdir
    else:
        work_dir = opts.run_id
    dirs = f.init_dirs(work_dir, opts)
    f.makedirs([work_dir, work_dir + '/STORAGE', work_dir + '/OUTPUT', dirs
        ['storage'], dirs['out'], dirs['delete'], dirs['log']])
    (design, target_list, target_bed, transcripts_list, cnv_target_list,
        cnv_target_bed, cnv_ref_ploidy, cnv_ref_calls) = f.panel_check(opts
        .panel, cfg)
    if opts.design != None:
        design = opts.design
    workflow = opts.workflow
    if workflow == 'ALL':
        workflow = 'ARMIBVFEC'
    if design == 'Amplicon':
        workflow = re.sub('MIB', '', workflow)
        workflow = re.sub('M', '', workflow)
    if opts.GATKBestPractices:
        workflow = re.sub('I', '', workflow)
    if opts.analysis == 'Germline':
        pipeline.Pipeline_Germline_Multisample(workflow, opts.samplesheet,
            design, opts.panel, dirs, cfg, opts, target_list, target_bed,
            transcripts_list, cnv_target_list, cnv_target_bed,
            cnv_ref_ploidy, cnv_ref_calls)
    if opts.analysis == 'GermlineSS':
        pipeline.Pipeline_Germline_Singlesample(workflow, opts.samplesheet,
            design, opts.panel, dirs, cfg, opts, target_list, target_bed,
            transcripts_list, cnv_target_list, cnv_target_bed,
            cnv_ref_ploidy, cnv_ref_calls)
    elif opts.analysis == 'SomaticCC':
        pipeline.Pipeline_Somatic_Case_Control(workflow, opts.samplesheet,
            design, opts.panel, dirs, cfg, opts, target_list, target_bed,
            transcripts_list, cnv_target_list, cnv_target_bed,
            cnv_ref_ploidy, cnv_ref_calls)
    elif opts.analysis == 'Somatic':
        pipeline.Pipeline_Somatic(workflow, opts.samplesheet, design, opts.
            panel, dirs, cfg, opts, target_list, target_bed,
            transcripts_list, cnv_target_list, cnv_target_bed,
            cnv_ref_ploidy, cnv_ref_calls)
    elapsed_time = divmod((datetime.datetime.now() - start_time).
        total_seconds(), 60)
    print('\nTime elapsed: %d min, %d sec' % elapsed_time)

import argparse
import subprocess
import json
import os
import textwrap
import random as rm
import datetime
import pysam
import random as r
import regex as re
import pipeline as pipeline
import functions as f


if __name__ == '__main__':

	parser = argparse.ArgumentParser('This is the Coolest Pipeline you have ever seen')
	parser.add_argument('-v', '--version', action='version', version='Powercall v3.2.0')

	parser.add_argument('-c', '--cfg', help="Configuration file in json format")
	parser.add_argument('-s', '--samplesheet', help="Samplesheet that contains filepaths and samples associated", required=True)
	parser.add_argument('-d', '--design', help="Design of the NGS experiment [Enrichment,Amplicon].",choices=['Enrichment','Amplicon'])
	parser.add_argument('-p', '--panel', help="Type of Panel used for the analysis [TrusightCardio (illumina), TrusightCancer (illumina), TrusightOne (illumina), BRCAMASTRDx (MULTIPLICOM), ALPORTMASTR (MULTIPLICOM), HTC (SophiaGenetics), CustomSSQXT (Custom SureSelect QXT Agilent), CustomHPHS (Custom HaloPlex HS Agilent), Custom (Other Custom panel), CCP17]",
		choices="[TrusightCardio, TrusightCancer, TrusightOne, BRCAMASTRDx, ALPORTMASTR, HCS, CustomSSQXT, CustomHPHS, Custom, CCP17]")
	parser.add_argument('-a', '--analysis', help="Type of analysis [Germline (Multisample), GermlineSS (Singlesample), SomaticCC (Case-Control), Somatic (only Case)].", choices=['Germline', 'GermlineSS','SomaticCC','Somatic'], default='Germline')
	parser.add_argument('-id','--run_id', help="Run id [YYYYMMDD_Run_NRUN_PANEL}", required=True)
	parser.add_argument('-w', '--workdir', help="Working Directory. Use this option if you want to work in a precise directory. Default: '/home/run_id'", default=None)
	parser.add_argument('--workflow', help="String that indicates which steps the analysis must do: A-> Alignment, R-> AddOrReplaceReadGroups, M-> MarkDuplicates, I-> IndelRealigner, B-> BaseRecalibrator, V-> Variant Calling, F-> Features Extraction, E-> Annotation. Es: --start AMIBVFE indicates all steps (like --start ALL), --start MIBV starts from MarkDuplicates and ends to Variant Calling. Default: ALL ", default='ALL')
	parser.add_argument('-BP', '--GATKBestPractices', help="GATK Best practices workflow", action='store_true')

	start_time = datetime.datetime.now()
	success = subprocess.call('clear')
	
	global opts
	opts = parser.parse_args()

	dirs=dict()
	
	if opts.cfg != None:
		cfg = json.loads((open(opts.cfg).read()).encode('utf8'))
	else:
		cfg = json.loads((open('/'.join(os.path.dirname(os.path.abspath(__file__)).split('/')[:-1]) + '/configs/Powercall.default.cfg.json').read()).encode('utf8'))
	
	if opts.workdir != None:
		work_dir = opts.workdir
	else:
		work_dir = opts.run_id

	dirs = f.init_dirs(work_dir,opts)
	f.makedirs([work_dir, work_dir+'/STORAGE', work_dir+'/OUTPUT', dirs['storage'], dirs['out'], dirs['delete'], dirs['log'], ])

	design,target_list,target_bed,transcripts_list,cnv_target_list,cnv_target_bed,cnv_ref_ploidy,cnv_ref_calls = f.panel_check(opts.panel,cfg)

	if opts.design != None:
		design = opts.design

	workflow = opts.workflow
	if workflow == 'ALL':
		workflow = 'ARMIBVFEC'

	if design == 'Amplicon':
		workflow=re.sub('MIB','',workflow)
		workflow=re.sub('M','',workflow)

	if opts.GATKBestPractices:
		workflow=re.sub('I','',workflow)

	if opts.analysis == 'Germline':
		pipeline.Pipeline_Germline_Multisample(workflow,opts.samplesheet,design,opts.panel,dirs,cfg,opts,target_list,target_bed,transcripts_list,cnv_target_list,cnv_target_bed,cnv_ref_ploidy,cnv_ref_calls)

	if opts.analysis == 'GermlineSS':
		pipeline.Pipeline_Germline_Singlesample(workflow,opts.samplesheet,design,opts.panel,dirs,cfg,opts,target_list,target_bed,transcripts_list,cnv_target_list,cnv_target_bed,cnv_ref_ploidy,cnv_ref_calls)

	elif opts.analysis == 'SomaticCC':
		pipeline.Pipeline_Somatic_Case_Control(workflow,opts.samplesheet,design,opts.panel,dirs,cfg,opts,target_list,target_bed,transcripts_list,cnv_target_list,cnv_target_bed,cnv_ref_ploidy,cnv_ref_calls)

	elif opts.analysis == 'Somatic':
		pipeline.Pipeline_Somatic(workflow,opts.samplesheet,design,opts.panel,dirs,cfg,opts,target_list,target_bed,transcripts_list,cnv_target_list,cnv_target_bed,cnv_ref_ploidy,cnv_ref_calls)

	elapsed_time = divmod((datetime.datetime.now() - start_time).total_seconds(),60)
	print("\nTime elapsed: %d min, %d sec" % elapsed_time)
