def main():
"""
Main configuration method made to be called if user starts this script on his own
"""
blue("Welcome to NGS configurator\n")
parser = argparse.ArgumentParser(description=blue("NGS configurator"))
parser.add_argument("-download", default=joiner("downloads"), help="path to download directory")
parser.add_argument("-hg", default=joiner("hg19"), help="path to hg19 reference files directory")
parser.add_argument(
"-1", dest="STAGE_1", action="store_true", help='set true if you want to run stage 1 - "actual alignment"'
)
parser.add_argument(
"-2", dest="STAGE_2", action="store_true", help='set true if you want to run stage 2 - "SAM to BAM conversion"'
)
parser.add_argument(
"-3", dest="STAGE_3", action="store_true", help='set true if you want to run stage 3 - "marking_PCR_duplicates"'
)
parser.add_argument(
"-4", dest="STAGE_4", action="store_true", help='set true if you want to run stage 4 - "local_realignment"'
)
parser.add_argument(
"-5",
dest="STAGE_5",
action="store_true",
help='set true if you want to run stage 5 - "quality score recalibration"',
)
parser.add_argument(
"-6", dest="STAGE_6", action="store_true", help='set true if you want to run stage 6 - "produce raw SNP calls"'
)
parser.add_argument(
"-all", dest="ALL_STAGES", action="store_true", help="set true if you want to run all stages one by one."
)
parser.add_argument("--seq-read-url", dest="SEQ_READ_URL", help="url to your input file")
args = parser.parse_args()
if args.SEQ_READ_URL:
if not download_file("input file", args.SEQ_READ_URL, joiner(args.hg, "chromFa")):
raise Exception("Something went wrong while downloading the input file")
with cwd(joiner(args.hg, "chromFa")):
run_command("gunzip -f " + args.SEQ_READ_URL.strip().split("/")[-1], Exception)
run_command(
"mv " + args.SEQ_READ_URL.strip().split("/")[-1].strip().split(".gz")[0] + " input.fastq", Exception
)
if args.ALL_STAGES:
blue("All stages to be processed.")
if args.STAGE_1 or args.ALL_STAGES:
actual_alignment(args)
if args.STAGE_2 or args.ALL_STAGES:
SAM_to_BAM_conversion(args)
if args.STAGE_3 or args.ALL_STAGES:
marking_PCR_duplicates(args)
if args.STAGE_4 or args.ALL_STAGES:
local_realignment(args)
if args.STAGE_5 or args.ALL_STAGES:
quality_score_recalibration(args)
if args.STAGE_6 or args.ALL_STAGES:
run_haplotype_caller(args)
def run_haplotype_caller(args):
blue("Going for STAGE_6 - run_haplotype_caller")
with cwd(joiner(args.hg, "chromFa")):
cmd = (
"module add "
+ ngs_tools_dict["GATK"]
+ " && $GATK_RUN -T HaplotypeCaller -R hg19.fa -I recal_reads.bam -L chr20 --genotyping_mode DISCOVERY -stand_call_conf 30 -stand_emit_conf 10 -o raw_variants.vcf"
)
run_command(cmd, Exception)
ok("Done!")
def marking_PCR_duplicates(args):
blue("Going for STAGE_3 - marking_PCR_duplicates")
with cwd(joiner(args.hg, "chromFa")):
cmd = (
"module add "
+ ngs_tools_dict["Picard"]
+ " && $PICARDRUN MarkDuplicates INPUT=output.bam OUTPUT=output.marked.bam METRICS_FILE=metrics CREATE_INDEX=true VALIDATION_STRINGENCY=LENIENT"
)
run_command(cmd, Exception)
ok("done")
def SAM_to_BAM_conversion(args):
blue("Going for STAGE_2 - SAM_to_BAM_conversion")
with cwd(joiner(args.hg, "chromFa")):
cmd = (
"module add "
+ ngs_tools_dict["Picard"]
+ " && $PICARDRUN SortSam SO=coordinate INPUT=out.sam OUTPUT=output.bam VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=true"
)
run_command(cmd, Exception)
ok("done")
def actual_alignment(args):
blue("Going for STAGE_1 - actual_alignment")
with cwd(joiner(args.hg, "chromFa")):
cmds = [
"module add " + ngs_tools_dict["bwa"] + " && bwa aln -t 4 -f input.sai hg19 input.fastq",
"module add "
+ ngs_tools_dict["bwa"]
+ ' && bwa samse -f out.sam -r "@RG\tID:bwa\tLB:Exome1Lib\tSM:Exome1Sampl\tPL:ILLUMINA" hg19 input.sai input.fastq',
]
run_commands(cmds, Exception)
ok("done")
def quality_score_recalibration(args):
blue("Going for STAGE_5 - quality_score_recalibration")
with cwd(joiner(args.hg, "chromFa")):
cmds = [
"module add "
+ ngs_tools_dict["GATK"]
+ " && $GATK_RUN -T BaseRecalibrator -R hg19.fa -I input_bam.marked.realigned.fixed.bam -L chr20 -knownSites dbsnp_138.hg19.vcf -o recal_data.table",
"module add "
+ ngs_tools_dict["GATK"]
+ " && $GATK_RUN -T PrintReads -R hg19.fa -I input_bam.marked.realigned.fixed.bam -L chr20 -BQSR recal_data.table -o recal_reads.bam",
]
run_commands(cmds, Exception)
ok("Done!")
def local_realignment(args):
blue("Going for STAGE_4 - local_realignment")
with cwd(joiner(args.hg, "chromFa")):
cmds = [
"module add "
+ ngs_tools_dict["GATK"]
+ " && $GATK_RUN -T RealignerTargetCreator -R hg19.fa -o input.bam.list -I output.marked.bam",
"module add "
+ ngs_tools_dict["GATK"]
+ " && $GATK_RUN -I output.marked.bam -R hg19.fa -T IndelRealigner -targetIntervals input.bam.list -o input.marked.realigned.bam",
"module add "
+ ngs_tools_dict["Picard"]
+ " && $PICARDRUN FixMateInformation INPUT=input.marked.realigned.bam OUTPUT=input_bam.marked.realigned.fixed.bam SO=coordinate VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=true",
]
run_commands(cmds, Exception)
ok("Done!")