for (sf, chr, locus, ref, alt), r in snvdata.iteritems():
chrom = chrreg.label2chrom(sf, chr)
assert (chrom)
snvkey = (chrom, locus, ref, alt)
if snvkey not in snvdata1:
snvdata1[snvkey] = (chrom, locus, ref, alt, r)
for bamfile in opt.alignments:
chrreg.add_bamlabels(bamfile)
chrreg.determine_chrom_order()
snvdata = sorted(snvdata1.values(),
key=lambda s: (chrreg.chrom_order(s[0]), s[1], s[2], s[3]))
# extrasnvheaders = filter(lambda h: h in usedsnvheaders, extrasnvheaders)
progress.message("SNVs: %d\n" % len(snvdata))
outheaders = snvheaders + filter(
None, """
SNVCountForward
SNVCountReverse
RefCountForward
RefCountReverse
SNVCount
RefCount
GoodReads
%BadRead
R
HomoVarSc
HetSc
HomoRefSc
sampsig = "".join(
map(str,
[1 * (len(types2files[t]) > 0)
for t in "GDNA SDNA NRNA TRNA".split()]))
if sampsig == "1111":
events = AllSamplesEvent
elif sampsig == "1100":
events = DNAOnlyEvent
elif sampsig == "1010":
events = NormalOnlyEvent
elif sampsig == "0111":
events = NoGDNAEvent
else:
raise RuntimeError("Bad combination of sample files")
progress.message("Testing for events: %s." % (", ".join(events.listall()), ))
events.setCounts(GDNA, SDNA, NRNA, TRNA)
cosmic_headers = []
if opt.cosmic:
progress.stage("Parsing COSMIC annotation file")
if opt.cosmic.endswith('.gz'):
f = gzip.open(opt.cosmic, mode='rt', encoding='utf8')
else:
f = open(opt.cosmic, mode='rt', encoding='utf8')
reader = csv.DictReader(f, delimiter='\t')
for cos in reader:
if cos['Mutation genome position']:
chr, locus = cos['Mutation genome position'].split(':', 1)
pos_st, pos_ed = locus.split('-', 1)
continue
if not re.search(r'^[ACGT](,[ACGT])*$', alt):
continue
for h in r:
if r.get(h):
usedsnpheaders.add(h)
cannonr = (",".join(map(lambda t: "%s:%s" % t, sorted(r.items()))))
snpkey = (chr, locus, ref, alt, cannonr)
if snpkey not in snpdata:
snpdata[snpkey] = (chr, locus, ref, alt, r)
progress.update()
progress.done()
snpdata = sorted(snpdata.values())
extrasnpheaders = filter(lambda h: h in usedsnpheaders, extrasnpheaders)
progress.message("SNPs: %d" % len(snpdata))
progress.stage("Read splice junction data", len(opt.junctions))
juncdata = set()
for juncfile in opt.junctions:
junc = BEDFile(filename=juncfile)
for r in junc:
chr = r['chrom']
st = int(r['chromStart'])
ed = int(r['chromEnd'])
bs = map(int, r['blockSizes'].split(','))
assert(len(bs) == 2)
gap = (st + bs[0], ed - bs[1])
key = (chr, gap)
juncdata.add(key)
progress.update()
snvdata1 = {}
for (sf, chr, locus, ref, alt), r in snvdata.iteritems():
chrom = chrreg.label2chrom(sf,chr)
assert(chrom)
snvkey = (chrom,locus,ref,alt)
if snvkey not in snvdata1:
snvdata1[snvkey] = (chrom,locus,ref,alt,r)
for bamfile in opt.alignments:
chrreg.add_bamlabels(bamfile)
chrreg.determine_chrom_order()
snvdata = sorted(snvdata1.values(),key=lambda s: (chrreg.chrom_order(s[0]),s[1],s[2],s[3]))
# extrasnvheaders = filter(lambda h: h in usedsnvheaders, extrasnvheaders)
progress.message("SNVs: %d\n" % len(snvdata))
outheaders = snvheaders + filter(None, """
SNVCountForward
SNVCountReverse
RefCountForward
RefCountReverse
SNVCount
RefCount
GoodReads
%BadRead
R
HomoVarSc
HetSc
HomoRefSc
VarDomSc
cmdargs = " ".join(args)
execution_log = """
readCounts Options:
ReadCounts Files (-c): %s
Matrix Output (-M): %s
Min. Reads (-m): %s%s
Quiet (-q): %s
Outfile File (-o): %s
Command-Line: readCountsMatrix %s
""" % (", ".join(opt.counts), None if not matrix else opt.matrix, opt.minreads,
"" if opt.matrix not in ("Ref:Var", "Ref;Var") or opt.minreads == 0 else
" (ignored)", opt.quiet, opt.output, cmdargs)
progress.message(execution_log)
from dataset import XLSFileTable, CSVFileTable, TSVFileTable, XLSXFileTable, TXTFileTable
progress.stage("Read ReadCounts input files", len(opt.counts))
headers = "CHROM POS REF ALT ReadGroup RefCount SNVCount GoodReads".split()
# NOTE: This *MUST* correspond to the columns in the readCounts .txt file output
txtheaders = "CHROM POS REF ALT ReadGroup SNVCountForward SNVCountReverse RefCountForward RefCountReverse SNVCount RefCount GoodReads".split(
)
allrg = set()
vafmatrix = defaultdict(dict)
for filename in opt.counts:
base, extn = filename.rsplit('.', 1)
extn = extn.lower()
if extn == 'csv':
if fatal:
sys.exit(1)
from event import *
sampsig = "".join(map(str,map(lambda t: 1*(len(types2files[t])>0),"GDNA SDNA NRNA TRNA".split())))
if sampsig == "1111":
events = AllSamplesEvent
elif sampsig == "1100":
events = DNAOnlyEvent
elif sampsig == "1010":
events = NormalOnlyEvent
elif sampsig == "0111":
events = NoGDNAEvent
else:
raise RuntimeError("Bad combination of sample files")
progress.message("Testing for events: %s."%(", ".join(events.listall()),))
events.setCounts(GDNA,SDNA,NRNA,TRNA)
cosmic_headers = []
if opt.cosmic:
progress.stage("Parsing COSMIC annotation file")
if opt.cosmic.endswith('.gz'):
f = gzip.open(opt.cosmic, 'r')
else:
f = open(opt.cosmic, 'r')
reader = csv.DictReader(f, delimiter='\t')
for cos in reader:
if cos['Mutation genome position']:
chr,locus = cos['Mutation genome position'].split(':',1)
pos_st,pos_ed = locus.split('-',1)
for juncfile in juncchroms:
chrreg.add_labels(juncfile, juncchroms[juncfile])
juncdata1 = set()
for jf, chr, gap in juncdata:
chrom = chrreg.label2chrom(jf, chr)
juncdata1.add((chrom, gap))
chrreg.determine_chrom_order()
snpdata = sorted(list(snvdata1.values()),
key=lambda s: (chrreg.chrom_order(s[0]), s[1], s[2], s[3]))
extrasnpheaders = [h for h in extrasnpheaders if h in usedsnpheaders]
progress.message("SNPs: %d" % len(snpdata))
juncdata = sorted(
((chr, gap[i], gap) for i in (0, 1) for chr, gap in juncdata1),
key=lambda j: (chrreg.chrom_order(j[0]), j[1], j[2]))
progress.message("Exon/Intron junctions: %d" % len(juncdata))
outheaders = snpheaders + [
_f for _f in """
NumofJuncs
Distance
Junctions
SNPJuncIntronCount
SNPJuncNoIntronCount
NoSNPJuncIntronCount
NoSNPJuncNoIntronCount
Advanced:
Min. Reads (-m) %s (applied only to VAF matrix)
Max. Reads (-M): %s
Read Groups (-G): %s%s
Threads per BAM (-t): %s
Quiet (-q): %s
Command-Line: scReadCounts %s
""" % (", ".join(opt.snvs), ", ".join(opt.alignments), opt.filter,
"" if readfilter == None else "\n" + indent(readfilter.tostr(), 10),
opt.output, opt.minreads, opt.maxreads,
None if readgroup == None else opt.readgroup, "" if readgroup == None
else "\n" + indent(readgroup.tostr(), 12), opt.tpb, opt.quiet, cmdargs)
progress.message(execution_log)
args = []
args.extend(["-s", " ".join(opt.snvs)])
args.extend(["-r", " ".join(opt.alignments)])
args.extend(["-f", opt.filter])
args.extend(["-o", opt.output])
args.extend(["-m", 0])
if opt.maxreads != maxreads_default:
args.extend(["-M", opt.maxreads])
if readgroup != None:
args.extend(["-G", opt.readgroup])
args.extend(["-t", opt.tpb])
if opt.quiet:
args.extend(["-q"])
args = [str(x) for x in args]
Unique Reads (-U): %s
Read Groups (-G): %s%s
Threads per BAM (-t): %s
Full Headers (-F): %s
Quiet (-q): %s
Debug (-d): %s
Command-Line: readCounts %s
""" % (", ".join(opt.snvs), ", ".join(
opt.alignments), opt.filter, "" if readfilter == None else "\n" +
indent(readfilter.tostr(), 10), opt.output, opt.minreads, opt.maxreads,
opt.unique, None if readgroup == None else opt.readgroup,
"" if readgroup == None else "\n" + indent(readgroup.tostr(), 12),
opt.tpb, opt.full, opt.quiet, opt.debug, cmdargs)
progress.message(execution_log)
if opt.maxreads == None:
opt.maxreads = 1e+20
from dataset import XLSFileTable, CSVFileTable, TSVFileTable, XLSXFileTable, TXTFileTable, BEDFile, VCFFile
progress.stage("Read SNV data", len(opt.snvs))
snvheaders = [_f for _f in """
CHROM POS REF ALT
""".split() if _f]
snvdata = {}
# extrasnvheaders = []
# usedsnvheaders = set()
snvchroms = defaultdict(set)
