def main(args):
print "INFO\t" + now(
) + "\tstarting " + sys.argv[0] + " called with args: " + ' '.join(
sys.argv) + "\n"
tmpbams = [
] # temporary BAMs, each holds the realigned reads for one mutation
exclfns = [
] # 'exclude' files store reads to be removed from the original BAM due to deletions
if not os.path.exists(args.bamFileName + '.bai'):
sys.stderr.write(
"ERROR\t" + now() +
"\tinput bam must be indexed, not .bai file found for " +
args.bamFileName + " \n")
sys.exit(1)
alignopts = {}
if args.alignopts is not None:
alignopts = dict([o.split(':') for o in args.alignopts.split(',')])
aligners.checkoptions(args.aligner, alignopts, None, sv=True)
# load insertion library if present
try:
if args.inslib is not None:
print "INFO\t" + now(
) + "\tloading insertion library from " + args.inslib
args.inslib = load_inslib(args.inslib)
except Exception, e:
sys.stderr.write("ERROR\t" + now() +
"\tfailed to load insertion library " + args.inslib +
"\n")
traceback.print_exc(file=sys.stderr)
sys.stderr.write("\n")
sys.exit(1)
def main(args):
print "INFO\t" + now() + "\tstarting " + sys.argv[0] + " called with args: " + " ".join(sys.argv) + "\n"
tmpbams = [] # temporary BAMs, each holds the realigned reads for one mutation
exclfns = [] # 'exclude' files store reads to be removed from the original BAM due to deletions
if not os.path.exists(args.bamFileName + ".bai"):
sys.stderr.write(
"ERROR\t" + now() + "\tinput bam must be indexed, not .bai file found for " + args.bamFileName + " \n"
)
sys.exit(1)
alignopts = {}
if args.alignopts is not None:
alignopts = dict([o.split(":") for o in args.alignopts.split(",")])
aligners.checkoptions(args.aligner, alignopts, None, sv=True)
# load insertion library if present
try:
if args.inslib is not None:
print "INFO\t" + now() + "\tloading insertion library from " + args.inslib
args.inslib = load_inslib(args.inslib)
except Exception, e:
sys.stderr.write("ERROR\t" + now() + "\tfailed to load insertion library " + args.inslib + "\n")
traceback.print_exc(file=sys.stderr)
sys.stderr.write("\n")
sys.exit(1)
def main(args):
print "INFO\t" + now() + "\tstarting " + sys.argv[0] + " called with args: " + ' '.join(sys.argv) + "\n"
bedfile = open(args.varFileName, 'r')
reffile = pysam.Fastafile(args.refFasta)
if not os.path.exists(args.bamFileName + '.bai'):
sys.stderr.write("ERROR\t" + now() + "\tinput bam must be indexed, not .bai file found for " + args.bamFileName + " \n")
sys.exit(1)
alignopts = {}
if args.alignopts is not None:
alignopts = dict([o.split(':') for o in args.alignopts.split(',')])
aligners.checkoptions(args.aligner, alignopts, args.picardjar)
# load readlist to avoid, if specified
avoid = None
if args.avoidreads is not None:
avoid = dictlist(args.avoidreads)
# make a temporary file to hold mutated reads
outbam_mutsfile = "addindel." + str(uuid4()) + ".muts.bam"
bamfile = pysam.Samfile(args.bamFileName, 'rb')
outbam_muts = pysam.Samfile(outbam_mutsfile, 'wb', template=bamfile)
outbam_muts.close()
bamfile.close()
tmpbams = []
if not os.path.exists(args.tmpdir):
os.mkdir(args.tmpdir)
print "INFO\t" + now() + "\tcreated tmp directory: " + args.tmpdir
if not os.path.exists('addindel_logs_' + os.path.basename(args.outBamFile)):
os.mkdir('addindel_logs_' + os.path.basename(args.outBamFile))
print "created directory: addindel_logs_" + os.path.basename(args.outBamFile)
assert os.path.exists('addindel_logs_' + os.path.basename(args.outBamFile)), "could not create output directory!"
assert os.path.exists(args.tmpdir), "could not create temporary directory!"
pool = Pool(processes=int(args.procs))
results = []
ntried = 0
for bedline in bedfile:
if ntried < int(args.numsnvs) or int(args.numsnvs) == 0:
c = bedline.strip().split()
chrom = c[0]
start = int(c[1])
end = int(c[2])
vaf = float(c[3])
type = c[4]
ins = None
assert type in ('INS', 'DEL')
if type == 'INS':
ins = c[5]
# make mutation (submit job to thread pool)
result = pool.apply_async(makemut, [args, chrom, start, end, vaf, ins, avoid, alignopts])
results.append(result)
ntried += 1
for result in results:
try:
tmpbamlist = result.get()
if tmpbamlist is not None:
for tmpbam in tmpbamlist:
tmpbams.append(tmpbam)
except AssertionError:
print "****************************************************"
print "* WARNING: assertion failed somewhere, check logs. *"
print "****************************************************"
tmpbams.sort()
# merge tmp bams
if len(tmpbams) == 1:
os.rename(tmpbams[0],outbam_mutsfile)
elif len(tmpbams) > 1:
mergebams(tmpbams,outbam_mutsfile,maxopen=int(args.maxopen))
bedfile.close()
# cleanup
for bam in tmpbams:
if os.path.exists(bam):
os.remove(bam)
if os.path.exists(bam + '.bai'):
os.remove(bam + '.bai')
if args.skipmerge:
print "INFO\t" + now() + "\tskipping merge, plase merge reads from", outbam_mutsfile, "manually."
else:
if args.tagreads:
from bs.markreads import markreads
tmp_tag_bam = 'tag.%s.bam' % str(uuid4())
markreads(mergedtmp, tmp_tag_bam)
move(tmp_tag_bam, mergedtmp)
print "INFO\t" + now() + "\ttagged reads."
print "INFO\t" + now() + "\tdone making mutations, merging mutations into", args.bamFileName, "-->", args.outBamFile
replace(args.bamFileName, outbam_mutsfile, args.outBamFile, seed=args.seed)
#cleanup
os.remove(outbam_mutsfile)
def main(args):
print "INFO\t" + now() + "\tstarting " + sys.argv[0] + " called with args: " + ' '.join(sys.argv) + "\n"
bedfile = open(args.varFileName, 'r')
reffile = pysam.Fastafile(args.refFasta)
if not os.path.exists(args.bamFileName + '.bai'):
sys.stderr.write("ERROR\t" + now() + "\tinput bam must be indexed, not .bai file found for " + args.bamFileName + " \n")
sys.exit(1)
alignopts = {}
if args.alignopts is not None:
alignopts = dict([o.split(':') for o in args.alignopts.split(',')])
aligners.checkoptions(args.aligner, alignopts, args.picardjar)
# load readlist to avoid, if specified
avoid = None
if args.avoidreads is not None:
avoid = dictlist(args.avoidreads)
# make a temporary file to hold mutated reads
outbam_mutsfile = "addsnv." + str(uuid4()) + ".muts.bam"
bamfile = pysam.Samfile(args.bamFileName, 'rb')
outbam_muts = pysam.Samfile(outbam_mutsfile, 'wb', template=bamfile)
outbam_muts.close()
bamfile.close()
tmpbams = []
if not os.path.exists(args.tmpdir):
os.mkdir(args.tmpdir)
print "INFO\t" + now() + "\tcreated tmp directory: " + args.tmpdir
if not os.path.exists('addsnv_logs_' + os.path.basename(args.outBamFile)):
os.mkdir('addsnv_logs_' + os.path.basename(args.outBamFile))
print "INFO\t" + now() + "\tcreated directory: addsnv_logs_" + os.path.basename(args.outBamFile)
assert os.path.exists('addsnv_logs_' + os.path.basename(args.outBamFile)), "could not create output directory!"
assert os.path.exists(args.tmpdir), "could not create temporary directory!"
pool = Pool(processes=int(args.procs))
results = []
ntried = 0
targets = []
for bedline in bedfile:
if ntried < int(args.numsnvs) or int(args.numsnvs) == 0:
c = bedline.strip().split()
target = {
'chrom' : c[0],
'start' : int(c[1]),
'end' : int(c[2]),
'vaf' : None,
'altbase' : None
}
# VAF is 4th column, if present
if len(c) > 3:
target['vaf'] = float(c[3])
# ALT is 5th column, if present
if len(c) == 5:
altbase = c[4].upper()
assert altbase in ['A','T','C','G'], "ERROR:\t" + now() + "\tALT " + altbase + " not A, T, C, or G!\n"
target['altbase'] = altbase
targets.append(target)
ntried += 1
targets = sorted(targets, key=itemgetter('chrom', 'start')) # sort list of dicts by chrom, start
haploclusters = []
hc = []
lastchrom = None
laststart = None
hapsize = int(args.haplosize)
for target in targets:
if lastchrom is None:
lastchrom = target['chrom']
laststart = target['start']
hc.append(target)
elif target['chrom'] == lastchrom:
if laststart is None:
laststart = target['start']
hc.append(target)
elif target['start'] - laststart < hapsize:
hc.append(target)
else:
haploclusters.append(hc)
hc = []
hc.append(target)
elif target['chrom'] != lastchrom:
haploclusters.append(hc)
hc = []
laststart = None
hc.append(target)
haploclusters.append(hc)
print "Debug, haploclusters:" + str(haploclusters)
for hc in haploclusters:
# make mutation (submit job to thread pool)
result = pool.apply_async(makemut, [args, hc, avoid, alignopts])
results.append(result)
for result in results:
tmpbamlist = result.get()
if tmpbamlist is not None:
for tmpbam in tmpbamlist:
tmpbams.append(tmpbam)
# merge tmp bams
if len(tmpbams) == 1:
move(tmpbams[0],outbam_mutsfile)
elif len(tmpbams) > 1:
mergebams(tmpbams,outbam_mutsfile,maxopen=int(args.maxopen))
bedfile.close()
# cleanup
for bam in tmpbams:
if os.path.exists(bam):
os.remove(bam)
if os.path.exists(bam + '.bai'):
os.remove(bam + '.bai')
if args.skipmerge:
print "INFO\t" + now() + "\tskipping merge, plase merge reads from", outbam_mutsfile, "manually."
else:
if args.tagreads:
from bs.markreads import markreads
tmp_tag_bam = 'tag.%s.bam' % str(uuid4())
markreads(mergedtmp, tmp_tag_bam)
move(tmp_tag_bam, mergedtmp)
print "INFO\t" + now() + "\ttagged reads."
print "INFO\t" + now() + "\tdone making mutations, merging mutations into", args.bamFileName, "-->", args.outBamFile
replace(args.bamFileName, outbam_mutsfile, args.outBamFile, seed=args.seed)
#cleanup
os.remove(outbam_mutsfile)
def main(args):
print "INFO\t" + now() + "\tstarting " + sys.argv[0] + " called with args: " + " ".join(sys.argv) + "\n"
bedfile = open(args.varFileName, "r")
reffile = pysam.Fastafile(args.refFasta)
if not os.path.exists(args.bamFileName + ".bai"):
sys.stderr.write(
"ERROR\t" + now() + "\tinput bam must be indexed, not .bai file found for " + args.bamFileName + " \n"
)
sys.exit(1)
alignopts = {}
if args.alignopts is not None:
alignopts = dict([o.split(":") for o in args.alignopts.split(",")])
aligners.checkoptions(args.aligner, alignopts, args.picardjar)
# load readlist to avoid, if specified
avoid = None
if args.avoidreads is not None:
avoid = dictlist(args.avoidreads)
# make a temporary file to hold mutated reads
outbam_mutsfile = "addsnv." + str(uuid4()) + ".muts.bam"
bamfile = pysam.Samfile(args.bamFileName, "rb")
outbam_muts = pysam.Samfile(outbam_mutsfile, "wb", template=bamfile)
outbam_muts.close()
bamfile.close()
tmpbams = []
if not os.path.exists(args.tmpdir):
os.mkdir(args.tmpdir)
print "INFO\t" + now() + "\tcreated tmp directory: " + args.tmpdir
if not os.path.exists("addsnv_logs_" + os.path.basename(args.outBamFile)):
os.mkdir("addsnv_logs_" + os.path.basename(args.outBamFile))
print "INFO\t" + now() + "\tcreated directory: addsnv_logs_" + os.path.basename(args.outBamFile)
assert os.path.exists("addsnv_logs_" + os.path.basename(args.outBamFile)), "could not create output directory!"
assert os.path.exists(args.tmpdir), "could not create temporary directory!"
pool = Pool(processes=int(args.procs))
results = []
ntried = 0
targets = []
for bedline in bedfile:
if ntried < int(args.numsnvs) or int(args.numsnvs) == 0:
c = bedline.strip().split()
target = {"chrom": c[0], "start": int(c[1]), "end": int(c[2]), "vaf": None, "altbase": None}
# VAF is 4th column, if present
if len(c) > 3:
target["vaf"] = float(c[3])
# ALT is 5th column, if present
if len(c) == 5:
altbase = c[4].upper()
assert altbase in ["A", "T", "C", "G"], (
"ERROR:\t" + now() + "\tALT " + altbase + " not A, T, C, or G!\n"
)
target["altbase"] = altbase
targets.append(target)
ntried += 1
targets = sorted(targets, key=itemgetter("chrom", "start")) # sort list of dicts by chrom, start
haploclusters = []
hc = []
lastchrom = None
laststart = None
hapsize = int(args.haplosize)
for target in targets:
if lastchrom is None:
lastchrom = target["chrom"]
laststart = target["start"]
hc.append(target)
elif target["chrom"] == lastchrom:
if laststart is None:
laststart = target["start"]
hc.append(target)
elif target["start"] - laststart < hapsize:
hc.append(target)
else:
haploclusters.append(hc)
hc = []
hc.append(target)
elif target["chrom"] != lastchrom:
haploclusters.append(hc)
hc = []
laststart = None
hc.append(target)
haploclusters.append(hc)
print "Debug, haploclusters:" + str(haploclusters)
for hc in haploclusters:
# make mutation (submit job to thread pool)
result = pool.apply_async(makemut, [args, hc, avoid, alignopts])
results.append(result)
for result in results:
tmpbamlist = result.get()
if tmpbamlist is not None:
for tmpbam in tmpbamlist:
tmpbams.append(tmpbam)
# merge tmp bams
if len(tmpbams) == 1:
move(tmpbams[0], outbam_mutsfile)
elif len(tmpbams) > 1:
mergebams(tmpbams, outbam_mutsfile, maxopen=int(args.maxopen))
bedfile.close()
# cleanup
for bam in tmpbams:
if os.path.exists(bam):
os.remove(bam)
if os.path.exists(bam + ".bai"):
os.remove(bam + ".bai")
if args.skipmerge:
print "INFO\t" + now() + "\tskipping merge, plase merge reads from", outbam_mutsfile, "manually."
else:
if args.tagreads:
from bs.markreads import markreads
tmp_tag_bam = "tag.%s.bam" % str(uuid4())
markreads(mergedtmp, tmp_tag_bam)
move(tmp_tag_bam, mergedtmp)
print "INFO\t" + now() + "\ttagged reads."
print "INFO\t" + now() + "\tdone making mutations, merging mutations into", args.bamFileName, "-->", args.outBamFile
replace(args.bamFileName, outbam_mutsfile, args.outBamFile, seed=args.seed)
# cleanup
os.remove(outbam_mutsfile)
def main(args):
print "INFO\t" + now() + "\tstarting " + sys.argv[0] + " called with args: " + ' '.join(sys.argv) + "\n"
bedfile = open(args.varFileName, 'r')
reffile = pysam.Fastafile(args.refFasta)
if not os.path.exists(args.bamFileName + '.bai'):
sys.stderr.write("ERROR\t" + now() + "\tinput bam must be indexed, not .bai file found for " + args.bamFileName + " \n")
sys.exit(1)
alignopts = {}
if args.alignopts is not None:
alignopts = dict([o.split(':') for o in args.alignopts.split(',')])
aligners.checkoptions(args.aligner, alignopts, args.samtofastq)
if args.numtargeted is not None:
if int(args.numsnvs) != 0 and int(args.numtargeted) > int(args.numsnvs):
# number of snvs tried cannot be smaller than number of snvs targeted
sys.stderr.write("WARNING\t" + now() + "\t --numtargeted ignored\n")
args.numtargeted = None
# load readlist to avoid, if specified
avoid = None
if args.avoidreads is not None:
avoid = dictlist(args.avoidreads)
# make a temporary file to hold mutated reads
outbam_mutsfile = "addsnv." + str(uuid4()) + ".muts.bam"
bamfile = pysam.Samfile(args.bamFileName, 'rb')
outbam_muts = pysam.Samfile(outbam_mutsfile, 'wb', template=bamfile)
outbam_muts.close()
bamfile.close()
tmpbams = []
if not os.path.exists(args.tmpdir):
os.mkdir(args.tmpdir)
print "INFO\t" + now() + "\tcreated tmp directory: " + args.tmpdir
if not os.path.exists('addsnv_logs_' + os.path.basename(args.outBamFile)):
os.mkdir('addsnv_logs_' + os.path.basename(args.outBamFile))
print "INFO\t" + now() + "\tcreated directory: addsnv_logs_" + os.path.basename(args.outBamFile)
assert os.path.exists('addsnv_logs_' + os.path.basename(args.outBamFile)), "could not create output directory!"
assert os.path.exists(args.tmpdir), "could not create temporary directory!"
pool = Pool(processes=int(args.procs))
results = []
nmutated = 0
ntried = 0
for bedline in bedfile:
if args.numtargeted is None:
continue_assert = ntried < int(args.numsnvs) or int(args.numsnvs) == 0
else:
continue_assert = nmutated < int(args.numtargeted) and (ntried < int(args.numsnvs) or int(args.numsnvs) == 0)
if continue_assert:
c = bedline.strip().split()
chrom = c[0]
start = int(c[1])
end = int(c[2])
vaf = None
altbase = None
# VAF is 4th column, if present
if len(c) > 3:
vaf = float(c[3])
# ALT is 5th column, if present
if len(c) == 5:
altbase = c[4].upper()
assert altbase in ['A','T','C','G'], "ERROR:\t" + now() + "\tALT " + altbase + " not A, T, C, or G!\n"
# make mutation (submit job to thread pool)
result = pool.apply_async(makemut, [args, chrom, start, end, vaf, altbase, avoid, alignopts])
if result.get() is not None and result.get():
# result = None if skipped
# result = [] if dropped because of nearby SNPs
nmutated += 1
results.append(result)
ntried += 1
for result in results:
tmpbamlist = result.get()
if tmpbamlist is not None:
for tmpbam in tmpbamlist:
tmpbams.append(tmpbam)
# merge tmp bams
if len(tmpbams) == 1:
move(tmpbams[0],outbam_mutsfile)
elif len(tmpbams) > 1:
mergebams(tmpbams,outbam_mutsfile,maxopen=int(args.maxopen))
bedfile.close()
# cleanup
for bam in tmpbams:
if os.path.exists(bam):
os.remove(bam)
if os.path.exists(bam + '.bai'):
os.remove(bam + '.bai')
if args.skipmerge:
print "INFO\t" + now() + "\tskipping merge, plase merge reads from", outbam_mutsfile, "manually."
else:
print "INFO\t" + now() + "\tdone making mutations, merging mutations into", args.bamFileName, "-->", args.outBamFile
replace(args.bamFileName, outbam_mutsfile, args.outBamFile)
#cleanup
os.remove(outbam_mutsfile)
def main(args):
print "INFO\t" + now() + "\tstarting " + sys.argv[0] + " called with args: " + ' '.join(sys.argv) + "\n"
bedfile = open(args.varFileName, 'r')
reffile = pysam.Fastafile(args.refFasta)
if not os.path.exists(args.bamFileName + '.bai'):
sys.stderr.write("ERROR\t" + now() + "\tinput bam must be indexed, not .bai file found for " + args.bamFileName + " \n")
sys.exit(1)
alignopts = {}
if args.alignopts is not None:
alignopts = dict([o.split(':') for o in args.alignopts.split(',')])
aligners.checkoptions(args.aligner, alignopts, args.samtofastq)
# load readlist to avoid, if specified
avoid = None
if args.avoidreads is not None:
avoid = dictlist(args.avoidreads)
# make a temporary file to hold mutated reads
outbam_mutsfile = "addindel." + str(uuid4()) + ".muts.bam"
bamfile = pysam.Samfile(args.bamFileName, 'rb')
outbam_muts = pysam.Samfile(outbam_mutsfile, 'wb', template=bamfile)
outbam_muts.close()
bamfile.close()
tmpbams = []
if not os.path.exists(args.tmpdir):
os.mkdir(args.tmpdir)
print "INFO\t" + now() + "\tcreated tmp directory: " + args.tmpdir
if not os.path.exists('addindel_logs_' + os.path.basename(args.outBamFile)):
os.mkdir('addindel_logs_' + os.path.basename(args.outBamFile))
print "created directory: addindel_logs_" + os.path.basename(args.outBamFile)
assert os.path.exists('addindel_logs_' + os.path.basename(args.outBamFile)), "could not create output directory!"
assert os.path.exists(args.tmpdir), "could not create temporary directory!"
pool = Pool(processes=int(args.procs))
results = []
ntried = 0
for bedline in bedfile:
if ntried < int(args.numsnvs) or int(args.numsnvs) == 0:
c = bedline.strip().split()
chrom = c[0]
start = int(c[1])
end = int(c[2])
vaf = float(c[3])
type = c[4]
ins = None
assert type in ('INS', 'DEL')
if type == 'INS':
ins = c[5]
# make mutation (submit job to thread pool)
result = pool.apply_async(makemut, [args, chrom, start, end, vaf, ins, avoid, alignopts])
results.append(result)
ntried += 1
for result in results:
try:
tmpbamlist = result.get()
if tmpbamlist is not None:
for tmpbam in tmpbamlist:
tmpbams.append(tmpbam)
except AssertionError:
print "****************************************************"
print "* WARNING: assertion failed somewhere, check logs. *"
print "****************************************************"
# merge tmp bams
if len(tmpbams) == 1:
os.rename(tmpbams[0],outbam_mutsfile)
elif len(tmpbams) > 1:
mergebams(tmpbams,outbam_mutsfile,maxopen=int(args.maxopen))
bedfile.close()
# cleanup
for bam in tmpbams:
if os.path.exists(bam):
os.remove(bam)
if os.path.exists(bam + '.bai'):
os.remove(bam + '.bai')
if args.skipmerge:
print "INFO\t" + now() + "\tskipping merge, plase merge reads from", outbam_mutsfile, "manually."
else:
print "INFO\t" + now() + "\tdone making mutations, merging mutations into", args.bamFileName, "-->", args.outBamFile
replace(args.bamFileName, outbam_mutsfile, args.outBamFile)
#cleanup
os.remove(outbam_mutsfile)
def main(args):
print "INFO\t" + now(
) + "\tstarting " + sys.argv[0] + " called with args: " + ' '.join(
sys.argv) + "\n"
bedfile = open(args.varFileName, 'r')
reffile = pysam.Fastafile(args.refFasta)
if not os.path.exists(args.bamFileName + '.bai'):
sys.stderr.write(
"ERROR\t" + now() +
"\tinput bam must be indexed, not .bai file found for " +
args.bamFileName + " \n")
sys.exit(1)
alignopts = {}
if args.alignopts is not None:
alignopts = dict([o.split(':') for o in args.alignopts.split(',')])
aligners.checkoptions(args.aligner, alignopts, args.samtofastq)
if args.numtargeted is not None:
if int(args.numsnvs) != 0 and int(args.numtargeted) > int(
args.numsnvs):
# number of snvs tried cannot be smaller than number of snvs targeted
sys.stderr.write("WARNING\t" + now() +
"\t --numtargeted ignored\n")
args.numtargeted = None
# load readlist to avoid, if specified
avoid = None
if args.avoidreads is not None:
avoid = dictlist(args.avoidreads)
# make a temporary file to hold mutated reads
outbam_mutsfile = "addsnv." + str(uuid4()) + ".muts.bam"
bamfile = pysam.Samfile(args.bamFileName, 'rb')
outbam_muts = pysam.Samfile(outbam_mutsfile, 'wb', template=bamfile)
outbam_muts.close()
bamfile.close()
tmpbams = []
if not os.path.exists(args.tmpdir):
os.mkdir(args.tmpdir)
print "INFO\t" + now() + "\tcreated tmp directory: " + args.tmpdir
if not os.path.exists('addsnv_logs_' + os.path.basename(args.outBamFile)):
os.mkdir('addsnv_logs_' + os.path.basename(args.outBamFile))
print "INFO\t" + now(
) + "\tcreated directory: addsnv_logs_" + os.path.basename(
args.outBamFile)
assert os.path.exists('addsnv_logs_' + os.path.basename(args.outBamFile)
), "could not create output directory!"
assert os.path.exists(args.tmpdir), "could not create temporary directory!"
pool = Pool(processes=int(args.procs))
results = []
nmutated = 0
ntried = 0
for bedline in bedfile:
if args.numtargeted is None:
continue_assert = ntried < int(args.numsnvs) or int(
args.numsnvs) == 0
else:
continue_assert = nmutated < int(args.numtargeted) and (
ntried < int(args.numsnvs) or int(args.numsnvs) == 0)
if continue_assert:
c = bedline.strip().split()
chrom = c[0]
start = int(c[1])
end = int(c[2])
vaf = None
altbase = None
# VAF is 4th column, if present
if len(c) > 3:
vaf = float(c[3])
# ALT is 5th column, if present
if len(c) == 5:
altbase = c[4].upper()
assert altbase in ['A', 'T', 'C', 'G'], "ERROR:\t" + now(
) + "\tALT " + altbase + " not A, T, C, or G!\n"
# make mutation (submit job to thread pool)
result = pool.apply_async(
makemut,
[args, chrom, start, end, vaf, altbase, avoid, alignopts])
if result.get() is not None and result.get():
# result = None if skipped
# result = [] if dropped because of nearby SNPs
nmutated += 1
results.append(result)
ntried += 1
for result in results:
tmpbamlist = result.get()
if tmpbamlist is not None:
for tmpbam in tmpbamlist:
tmpbams.append(tmpbam)
# merge tmp bams
if len(tmpbams) == 1:
move(tmpbams[0], outbam_mutsfile)
elif len(tmpbams) > 1:
mergebams(tmpbams, outbam_mutsfile, maxopen=int(args.maxopen))
bedfile.close()
# cleanup
for bam in tmpbams:
if os.path.exists(bam):
os.remove(bam)
if os.path.exists(bam + '.bai'):
os.remove(bam + '.bai')
if args.skipmerge:
print "INFO\t" + now(
) + "\tskipping merge, plase merge reads from", outbam_mutsfile, "manually."
else:
print "INFO\t" + now(
) + "\tdone making mutations, merging mutations into", args.bamFileName, "-->", args.outBamFile
replace(args.bamFileName, outbam_mutsfile, args.outBamFile)
#cleanup
os.remove(outbam_mutsfile)