parser.add_argument('--mask_start',
default=100,
help='number of bases to mask at start of genome')
parser.add_argument('--mask_end',
default=50,
help='number of bases to mask at end of genome')
if len(sys.argv) == 1:
parser.print_help(sys.stderr)
sys.exit(1)
args = parser.parse_args()
qc_line = {}
qc_line.update(
qc.get_total_variants(file=args.variants,
reference=args.reference,
indel=args.indel,
mask_start=int(args.mask_start),
mask_end=int(args.mask_end)))
qc_line.update(qc.get_qc_data(file=args.qc))
qc_line.update(qc.get_coverage_stats(file=args.coverage))
qc_line.update(qc.count_iupac_in_fasta(fasta=args.fasta))
try:
meta_data = qc.import_metadata(file=args.meta)
qc_line['ct'] = meta_data[qc_line['sample_name']]['ct']
qc_line['date'] = meta_data[qc_line['sample_name']]['date']
except:
qc_line['ct'] = 'NA'
qc_line['date'] = 'NA'
qc.write_qc_summary_header()
qc.write_qc_summary(summary=qc_line)
import sys
from ncov.parser.qc import create_qc_summary_line, write_qc_summary, \
write_qc_summary_header, import_ct_data
parser = argparse.ArgumentParser(description="Tool for summarizing QC data")
parser.add_argument('-c', '--qc', help='<sample>.qc.csv file to process')
parser.add_argument('-v', '--variants', \
help='<sample>.variants.tsv file to process')
parser.add_argument('-e', '--coverage', \
help='<sample>.per_base_coverage.bed file to process')
parser.add_argument('-i', '--indel', action='store_true', \
help='flag to determine whether to count indels')
parser.add_argument('-m', '--meta', \
help='full path to the metadata YAML file')
if len(sys.argv) == 1:
parser.print_help(sys.stderr)
sys.exit(1)
args = parser.parse_args()
ct_data = import_ct_data(file=args.meta)
qc_line = create_qc_summary_line(var_file=args.variants,
qc_file=args.qc,
cov_file=args.coverage,
meta_file=args.meta,
indel=args.indel)
write_qc_summary_header()
write_qc_summary(summary=qc_line)