recs = [r for r in reader]
vc = VC.MPileUPVariant(recs,
min_cov=MIN_COVERAGE,
err_sub=ERR_SUB,
expected_strand=args.strand,
pval_cutoff=args.pval_cutoff)
vc.call_variant()
print(vc.variant)
if len(vc.variant) == 0:
os.system("touch {out}.NO_SNPS_FOUND".format(out=args.output_prefix))
print("No SNPs found. END.", file=sys.stderr)
sys.exit(0)
# (2) for each CCS read, assign a haplotype (or discard if outlier)
pp = VariantPhaser.VariantPhaser(vc)
pp.phase_variant(args.sam_filename,
args.fastx_filename,
args.output_prefix,
partial_ok=args.partial_ok)
pp.haplotypes
pp.haplotypes.get_haplotype_vcf_assignment()
# (3) phase isoforms
seqids = set([
r.id for r in SeqIO.parse(open(args.fastx_filename),
VariantPhaser.type_fa_or_fq(args.fastx_filename))
])
isoform_tally = VariantPhaser.phase_isoforms(args.read_stat, seqids, pp)
if len(isoform_tally) == 0:
os.system("touch {out}.NO_HAPS_FOUND".format(out=args.output_prefix))
vc.call_variant()
print vc.variant
if len(vc.variant) == 0:
os.system("touch {out}.NO_SNPS_FOUND".format(out=args.output_prefix))
print >> sys.stderr, "No SNPs found. END."
sys.exit(0)
# (2) for each CCS read, assign a haplotype (or discard if outlier)
pp = VariantPhaser.VariantPhaser(vc)
pp.phase_variant(args.sam_filename, args.fastx_filename, args.output_prefix, partial_ok=args.partial_ok)
pp.haplotypes
pp.haplotypes.get_haplotype_vcf_assignment()
# (3) phase isoforms
seqids = set([r.id for r in SeqIO.parse(open(args.fastx_filename), VariantPhaser.type_fa_or_fq(args.fastx_filename))])
isoform_tally = VariantPhaser.phase_isoforms(args.read_stat, seqids, pp)
if len(isoform_tally) == 0:
os.system("touch {out}.NO_HAPS_FOUND".format(out=args.output_prefix))
print >> sys.stderr, "No good haps found. END."
sys.exit(0)
pp.haplotypes.write_haplotype_to_vcf(args.mapping_filename, isoform_tally, args.output_prefix)
# (4) clean isoforms
hap_count = VariantPhaseCleaner.make_haplotype_counts(isoform_tally)
# (5) error correct haplotypes
# if diploid, use exhaustive search
# otherwise, use hap counts (ToDo: make this work with exhaustive search later)
variants = [ [base.upper() for base,count in vc.variant[pos]] for pos in pp.accepted_pos]
# (1) read the mpileup and vall variants
reader = sp.MPileUpReader(args.mpileup_filename)
recs = [r for r in reader]
vc = VC.MPileUPVariant(recs, min_cov=MIN_COVERAGE, err_sub=ERR_SUB, expected_strand=args.strand, pval_cutoff=args.pval_cutoff)
vc.call_variant()
print vc.variant
if len(vc.variant) == 0:
os.system("touch {out}.NO_SNPS_FOUND".format(out=args.output_prefix))
print >> sys.stderr, "No SNPs found. END."
sys.exit(0)
# (2) for each CCS read, assign a haplotype (or discard if outlier)
pp = VariantPhaser.VariantPhaser(vc)
pp.phase_variant(args.sam_filename, args.fasta_filename, args.output_prefix, partial_ok=args.partial_ok)
pp.haplotypes
pp.haplotypes.get_haplotype_vcf_assignment()
# (3) phase isoforms
seqids = set([r.id for r in SeqIO.parse(open(args.fasta_filename), 'fasta')])
isoform_tally = VariantPhaser.phase_isoforms(args.read_stat, seqids, pp)
if len(isoform_tally) == 0:
os.system("touch {out}.NO_HAPS_FOUND".format(out=args.output_prefix))
print >> sys.stderr, "No good haps found. END."
sys.exit(0)
pp.haplotypes.write_haplotype_to_vcf(args.mapping_filename, isoform_tally, args.output_prefix)
# (4) clean isoforms
hap_count = VariantPhaseCleaner.make_haplotype_counts(isoform_tally)
os.remove(file)
# (1) read the mpileup and vall variants
reader = sp.MPileUpReader(args.mpileup_filename)
recs = [r for r in reader]
vc = VC.MPileUPVariant(recs, min_cov=MIN_COVERAGE, err_sub=ERR_SUB, expected_strand=args.strand, pval_cutoff=args.pval_cutoff)
vc.call_variant()
print(vc.variant)
if len(vc.variant) == 0:
os.system("touch {out}.NO_SNPS_FOUND".format(out=args.output_prefix))
print("No SNPs found. END.", file=sys.stderr)
sys.exit(0)
# (2) for each CCS read, assign a haplotype (or discard if outlier)
pp = VariantPhaser.VariantPhaser(vc)
pp.phase_variant(args.sam_filename, args.fastx_filename, args.output_prefix, partial_ok=args.partial_ok)
pp.haplotypes
pp.haplotypes.get_haplotype_vcf_assignment()
# (3) phase isoforms
seqids = set([r.id for r in SeqIO.parse(open(args.fastx_filename), VariantPhaser.type_fa_or_fq(args.fastx_filename))])
isoform_tally = VariantPhaser.phase_isoforms(args.read_stat, seqids, pp)
if len(isoform_tally) == 0:
os.system("touch {out}.NO_HAPS_FOUND".format(out=args.output_prefix))
print("No good haps found. END.", file=sys.stderr)
sys.exit(0)
pp.haplotypes.write_haplotype_to_vcf(args.mapping_filename, isoform_tally, args.output_prefix)
# (4) clean isoforms
hap_count = VariantPhaseCleaner.make_haplotype_counts(isoform_tally)
def main(args, parser):
args = parser.parse_args()
if args.bhFDR is not None:
print(
"--bhFDR {0} is given! Will be using Benjamini–Hochberg correction insteaad. --pval_cutoff is ignored."
.format(args.bhFDR))
# remove potential past run output
past_files = [
args.output + '.NO_SNPS_FOUND', args.output + '.NO_HAPS_FOUND',
args.output + '.snps', args.output + '.log',
args.output + '.human_readable.txt', args.output + '.vcf',
args.output + '.cleaned.human_readable.txt',
args.output + '.cleaned.vcf'
]
for file in past_files:
if os.path.exists(file):
os.remove(file)
snpsfound = False
# (0) generate pileups
f_human1 = open(args.output + '.human_readable_by_pos.txt', 'w')
f_human1.write("haplotype\thapIdx\tcontig\tpos\tvarIdx\tbase\tcount\n")
f_human2 = open(args.output + '.human_readable_by_hap.txt', 'w')
f_human2.write("haplotype\thapIdx\tcontig\tcount\n")
for mpileupFile, contig, start, end in elitePileups(
args.bamfile, args.genes, args.assembly, args.output):
# (1) read the mpileup and vall variants
reader = sam.MPileUpReader(mpileupFile)
recs = [r for r in reader]
vc = VC.MagMPileUPVariant(recs,
min_cov=MIN_COVERAGE,
err_sub=ERR_SUB,
expected_strand='+-',
pval_cutoff=args.pval_cutoff,
bhFDR=args.bhFDR)
vc.call_variant()
print(vc.variant)
if len(vc.variant) != 0:
snpsfound = True
else:
continue
# we write SNPs with the bases separated by "/" not "|" becuz we haven't phased them yet
with open(args.output + '.snps', 'a+') as f_snp:
for pos, v in vc.variant.items():
f_snp.write("{contig}\t{pos}\t{bases}\t{counts}\n".format(\
contig=contig,\
pos=pos+1,\
bases="/".join([b for (b,c) in v]),\
counts="/".join([str(c) for (b,c) in v])))
# (2) for each CCS read, assign a haplotype (or discard if outlier)
pp = VariantPhaser.MagVariantPhaser(vc)
pp.phase_variant(args.bamfile, [contig, start, end],
args.output,
partial_ok=True)
print(pp.haplotypes)
pp.haplotypes.get_haplotype_vcf_assignment()
pp.haplotypes.write_haplotype_to_humanreadable(contig, f_human1,
f_human2,
pp.seq_hap_info)
os.remove(mpileupFile)
f_human1.close()
f_human2.close()
if not snpsfound:
os.system("touch {out}.NO_SNPS_FOUND".format(out=args.output))
os.remove(args.output + '.human_readable.txt')
print("No SNPs found. END.", file=sys.stderr)
recs = [r for r in reader]
vc = VC.MPileUPVariant(recs,
min_cov=MIN_COVERAGE,
err_sub=ERR_SUB,
expected_strand=args.strand,
pval_cutoff=args.pval_cutoff)
vc.call_variant()
print(vc.variant)
if len(vc.variant) == 0:
os.system("touch {out}.NO_SNPS_FOUND".format(out=args.output_prefix))
print("No SNPs found. END.", file=sys.stderr)
sys.exit(0)
# (2) for each CCS read, assign a haplotype (or discard if outlier)
pp = VariantPhaser.VariantPhaser(vc)
pp.phase_variant(args.sam_filename,
args.fastx_filename,
args.output_prefix,
partial_ok=args.partial_ok)
pp.haplotypes
pp.haplotypes.get_haplotype_vcf_assignment()
# (3) phase isoforms -- not needed for this analysis!
#seqids = set([r.id for r in SeqIO.parse(open(args.fastx_filename), VariantPhaser.type_fa_or_fq(args.fastx_filename))])
#isoform_tally = VariantPhaser.phase_isoforms(args.read_stat, seqids, pp)
#if len(isoform_tally) == 0:
# os.system("touch {out}.NO_HAPS_FOUND".format(out=args.output_prefix))
# print("No good haps found. END.", file=sys.stderr)
# sys.exit(0)
pp.haplotypes.write_haplotype_to_vcf(args.mapping_filename, isoform_tally,