def main():
"""Evaluate Canvas results on simulated data"""
parser = OptionParser()
parser.add_option("-s", "--canvas_sim_id", dest="canvas_sim_id", type="string", help="simulation id (find Canvas results directories strating with sim_id")
parser.add_option("-d", "--canvas_sim_dir", dest="canvas_sim_dir", type="string", help="Canvas results directory")
(options, args) = parser.parse_args()
if options.canvas_sim_dir is None and options.canvas_sim_id is None:
parser.error("Specify Canvas results simulation id or directory")
if options.canvas_sim_dir is not None and options.canvas_sim_id is not None:
parser.error("Canvas results simulation id and directory are mutually exclusive options")
if options.canvas_sim_dir is not None:
res_dirs = [options.canvas_sim_dir]
if options.canvas_sim_id is not None:
canvas_dir = "/illumina/scratch/tmp/users/ccolombo/Canvas/"
res_dirs = [canvas_dir + cdir for cdir in os.listdir(canvas_dir) if os.path.isdir((canvas_dir + cdir)) and cdir.startswith(options.canvas_sim_id)]
if len(res_dirs) == 0:
print "No Canvas results directories found"
hg_file = "/home/ccolombo/filtered_human.hg19.genome"
for res_dir in res_dirs:
print res_dir
sim_dir = re.sub("/Canvas/", "/simulation/", res_dir)
res_id = re.sub("sim", "ev", res_dir.split("/")[-1])
if not os.path.exists(res_dir):
print("\nCanvas results directory %s does not exist\n\n" % res_dir)
continue
if not os.path.exists(res_dir):
print("\nSimulation directory %s does not exist\n\n" % sim_dir)
continue
if os.path.basename(res_dir).startswith("simNorm") or res_dir.endswith("_purity100"):
continue
out_dir = os.path.join("/illumina/scratch/tmp/users/ccolombo/evaluation/EvaluateCNV", res_id)
if not os.path.exists(out_dir):
os.mkdir(out_dir)
truth_file = create_het_cn_file(sim_dir, os.path.join(out_dir, "het_truth_file.bed"), no_dipl=True, hap_split=True, round=True)
#truth_file = "/illumina/scratch/tmp/users/ccolombo/simulation/HCC2218flt.bed"
truth_file = add_BED_complement(truth_file, hg_file, sort=False, out_dir=out_dir, hap_split=True)
perc_file = create_var_perc_file(sim_dir, os.path.join(out_dir, "var_perc.bed"), no_dipl=True)
# Write simulation parameters to file
out_file = os.path.join(out_dir, res_id + "_par.txt")
if not os.path.exists(out_file):
get_sim_params(sim_dir, truth_file, perc_file, out_file, hg_file)
# Run EvaluateCNV
out_file = os.path.join(out_dir, res_id + ".txt")
excl_file = "/illumina/scratch/tmp/users/ccolombo/evaluation/sim_filter.bed"
if not os.path.exists(out_file):
#if True:
evaluate_CNV(res_dir, truth_file, excl_file, out_file)
# Run EvaluateCNV only on heterogeneous variants
out_file = os.path.join(out_dir, res_id + "_onlyhet.txt")
#if True:
if not os.path.exists(out_file):
with open(excl_file, "r") as ef:
excl_vars = ef.readlines()
with open(perc_file, "r") as pf:
for line in pf:
(chr_id, start, end, cnA, cnB, perc) = line.strip().split("\t")
if float(perc) >= 0.8 and chr_id not in ["chrX", "chrY", "chrM"]:
excl_vars.append("\t".join([chr_id, start, end]) + "\n")
os.system("rm %s" % (perc_file))
excl_file = os.path.join(out_dir, "filter_onlyhet.bed")
with open(excl_file, "w") as wf:
wf.writelines(excl_vars)
evaluate_CNV(res_dir, truth_file, excl_file, out_file)
def create_ev_cov_files(cnv_file, cnv_type, part_file, out_dir, out_filename,
tumor_purity, excl_file, save_tmp, add_perc, add_shift,
hg_file):
out_file = os.path.join(out_dir, out_filename)
out_file_bin = re.sub(".bed$", "_bin.bed", out_file)
hap_coverage = 0
if cnv_type == "canvas":
cnv_file, tumor_purity, hap_coverage = init_param_canvas_file(
cnv_file, out_file)
elif cnv_type == "truth":
cnv_file = init_param_truth_file(cnv_file, out_dir, hg_file)
rm_files = [cnv_file]
print "Tumor purity: %f" % tumor_purity
# Exclude regions
if excl_file is not None:
if not os.path.exists(excl_file):
print "File for excluded regions %s does not exist\n" % excl_file
else:
cmd = "/illumina/thirdparty/bedtools/bedtools2-2.22.1/bin/bedtools subtract"
cmd += " -a %s" % cnv_file
cmd += " -b %s" % excl_file
cnv_file = run_bedtools_cmd(cmd, cnv_file, "_excl")
rm_files.append(cnv_file)
# Extract partitioned file
extr_part_file = re.sub(".bed$", "_partitioned.bed", out_file)
pc = subprocess.Popen("gunzip -c %s > %s" % (part_file, extr_part_file),
shell=True)
pc.wait()
# Intersect variants file with bin file
cmd = "/illumina/thirdparty/bedtools/bedtools2-2.22.1/bin/bedtools intersect"
cmd += " -a %s" % cnv_file
cmd += " -b %s" % extr_part_file
cmd += " -wa -wb"
intersect_file = run_bedtools_cmd(cmd, out_file, "_int")
rm_files.extend([intersect_file, extr_part_file])
with open(intersect_file, "r") as ifile:
int_lines = ifile.readlines()
if hap_coverage == 0:
hap_coverage = numpy.median([
float(int_line.strip().split("\t")[7])
for int_line in int_lines
if float(int_line.strip().split("\t")[3]) == 2
]) / 2
print "Haplotype coverage: %f (median)" % hap_coverage
wlines = ["#chr\tstart\tend\tCN\tobservedCoverage\texpectedCoverage"]
for int_line in int_lines:
(chr_segm, start_segm, end_segm, cn_segm, chr_bin, start_bin,
end_bin, cov_bin, segm_bin) = int_line.strip().split("\t")
expected_coverage = round((float(cn_segm) * tumor_purity + 2 *
(1 - tumor_purity)) * hap_coverage, 3)
wlines.append("\t".join([
chr_bin, start_bin, end_bin, cn_segm, cov_bin,
str(expected_coverage)
]))
with open(out_file_bin, "w") as ofile:
ofile.writelines("\n".join(wlines))
# # Sort chromosome intersect file
# cmd = "/illumina/thirdparty/bedtools/bedtools2-2.22.1/bin/bedtools sort"
# cmd += " -i %s" % intersect_file
# sorted_file = run_bedtools_cmd(cmd, out_file, "_sort")
# rm_files.append(sorted_file)
# Sort chromosome intersect file
cmd = "sort -k 1,1 -k2,2n %s" % intersect_file
sorted_file = run_bedtools_cmd(cmd, out_file, "_sort")
rm_files.append(sorted_file)
# Merge intersect file (median observed coverage)
cmd = "/illumina/thirdparty/bedtools/bedtools2-2.22.1/bin/bedtools merge"
cmd += " -i %s" % intersect_file
cmd += " -d -1"
cmd += " -c 4,8"
cmd += " -o mean,median"
merged_file = run_bedtools_cmd(cmd, intersect_file, "_merg")
rm_files.append(merged_file)
# Calculate expected coverage for each segment
with open(merged_file, "r") as mfile:
wlines = ["#chr\tstart\tend\tCN\tobservedCoverage\texpectedCoverage"]
for cnv_line in mfile.readlines():
(chrid, start, end, cn, cov) = cnv_line.strip().split("\t")
expected_coverage = round((float(cn) * tumor_purity + 2 *
(1 - tumor_purity)) * hap_coverage, 3)
wlines.append(cnv_line.strip() + "\t" + str(expected_coverage))
with open(out_file, "w") as ofile:
ofile.writelines("\n".join(wlines))
# Calculate expected coverage for each segment with shifted
cn_shift_suffix = []
if add_shift:
for cn_shift in [-2, -1, 1, 2]:
with open(merged_file, "r") as mfile:
wlines = [
"#chr\tstart\tend\tCN\tobservedCoverage\texpectedCovearge"
]
for cnv_line in mfile.readlines():
(chrid, start, end, cn, cov) = cnv_line.strip().split("\t")
expected_coverage = round(
((float(cn) + cn_shift) * tumor_purity + 2 *
(1 - tumor_purity)) * hap_coverage, 3)
wlines.append(cnv_line.strip() + "\t" +
str(expected_coverage))
cn_shift_suffix.append("_CNshift_" + str(cn_shift))
with open(
re.sub(".bed$", cn_shift_suffix[-1] + ".bed",
out_file), "w") as ofile:
ofile.writelines("\n".join(wlines))
# Remove temporary files
if not save_tmp:
for rmf in rm_files:
print "rm %s" % os.path.join(out_dir, rmf)
subprocess.Popen("rm %s" % os.path.join(out_dir, rmf), shell=True)
print "Output bed file written"
if add_perc:
if os.path.basename(out_file)[:-4].endswith("_truth"):
sim_dir = "/illumina/scratch/tmp/users/ccolombo/simulation/" + os.path.basename(
out_file)[4:-10]
else:
sim_dir = "/illumina/scratch/tmp/users/ccolombo/simulation/" + os.path.basename(
out_file)[4:-4]
if os.path.exists(sim_dir):
# For each variant: clonal percentage, coverage of overlapping segments
perc_file = create_var_perc_file(sim_dir, None, True)
cmd = "/illumina/thirdparty/bedtools/bedtools2-2.22.1/bin/bedtools intersect"
cmd += " -a %s" % perc_file
cmd += " -b %s" % out_file
cmd += " -wa -wb"
run_bedtools_cmd(cmd, out_file, "_perc")
# For the whole genome: clonal percentage, coverage of overlapping bins
cmd = "/illumina/thirdparty/bedtools/bedtools2-2.22.1/bin/bedtools complement"
cmd += " -i %s" % perc_file
cmd += " -g %s" % hg_file
pc = subprocess.Popen(cmd,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
shell=True)
compl = pc.stdout.readlines()
with open(perc_file, "r") as pbed:
lines = pbed.readlines()
for line in compl:
lines.append("\n" + line.rstrip() + "\t" + str(1) + "\t" +
str(1) + "\t" + str(1.0))
with open(perc_file, "w") as pbed:
pbed.writelines(lines)
cmd = "/illumina/thirdparty/bedtools/bedtools2-2.22.1/bin/bedtools intersect"
cmd += " -a %s" % perc_file
cmd += " -b %s" % out_file_bin
cmd += " -wa -wb"
run_bedtools_cmd(cmd, out_file_bin, "_perc_all")
print("rm %s" % perc_file)
subprocess.Popen("rm %s" % perc_file, shell=True)
print "Output bed file with variants percentages written"
else:
print "Cannot find simulation directory"
def create_ev_cov_files(cnv_file, cnv_type, part_file, out_dir, out_filename, tumor_purity, excl_file, save_tmp, add_perc, add_shift, hg_file):
out_file = os.path.join(out_dir, out_filename)
out_file_bin = re.sub(".bed$", "_bin.bed", out_file)
hap_coverage = 0
if cnv_type == "canvas":
cnv_file, tumor_purity, hap_coverage = init_param_canvas_file(cnv_file, out_file)
elif cnv_type == "truth":
cnv_file = init_param_truth_file(cnv_file, out_dir, hg_file)
rm_files = [cnv_file]
print "Tumor purity: %f" % tumor_purity
# Exclude regions
if excl_file is not None:
if not os.path.exists(excl_file):
print "File for excluded regions %s does not exist\n" % excl_file
else:
cmd = "/illumina/thirdparty/bedtools/bedtools2-2.22.1/bin/bedtools subtract"
cmd += " -a %s" % cnv_file
cmd += " -b %s" % excl_file
cnv_file = run_bedtools_cmd(cmd, cnv_file, "_excl")
rm_files.append(cnv_file)
# Extract partitioned file
extr_part_file = re.sub(".bed$", "_partitioned.bed", out_file)
pc = subprocess.Popen("gunzip -c %s > %s" % (part_file, extr_part_file), shell=True)
pc.wait()
# Intersect variants file with bin file
cmd = "/illumina/thirdparty/bedtools/bedtools2-2.22.1/bin/bedtools intersect"
cmd += " -a %s" % cnv_file
cmd += " -b %s" % extr_part_file
cmd += " -wa -wb"
intersect_file = run_bedtools_cmd(cmd, out_file, "_int")
rm_files.extend([intersect_file, extr_part_file])
with open(intersect_file, "r") as ifile:
int_lines = ifile.readlines()
if hap_coverage==0:
hap_coverage = numpy.median([float(int_line.strip().split("\t")[7]) for int_line in int_lines if float(int_line.strip().split("\t")[3])==2])/2
print "Haplotype coverage: %f (median)" % hap_coverage
wlines = ["#chr\tstart\tend\tCN\tobservedCoverage\texpectedCoverage"]
for int_line in int_lines:
(chr_segm, start_segm, end_segm, cn_segm, chr_bin, start_bin, end_bin, cov_bin, segm_bin) = int_line.strip().split("\t")
expected_coverage = round((float(cn_segm)*tumor_purity + 2*(1-tumor_purity)) * hap_coverage, 3)
wlines.append("\t".join([chr_bin, start_bin, end_bin, cn_segm, cov_bin, str(expected_coverage)]))
with open(out_file_bin, "w") as ofile:
ofile.writelines("\n".join(wlines))
# # Sort chromosome intersect file
# cmd = "/illumina/thirdparty/bedtools/bedtools2-2.22.1/bin/bedtools sort"
# cmd += " -i %s" % intersect_file
# sorted_file = run_bedtools_cmd(cmd, out_file, "_sort")
# rm_files.append(sorted_file)
# Sort chromosome intersect file
cmd = "sort -k 1,1 -k2,2n %s" % intersect_file
sorted_file = run_bedtools_cmd(cmd, out_file, "_sort")
rm_files.append(sorted_file)
# Merge intersect file (median observed coverage)
cmd = "/illumina/thirdparty/bedtools/bedtools2-2.22.1/bin/bedtools merge"
cmd += " -i %s" % intersect_file
cmd += " -d -1"
cmd += " -c 4,8"
cmd += " -o mean,median"
merged_file = run_bedtools_cmd(cmd, intersect_file, "_merg")
rm_files.append(merged_file)
# Calculate expected coverage for each segment
with open(merged_file, "r") as mfile:
wlines = ["#chr\tstart\tend\tCN\tobservedCoverage\texpectedCoverage"]
for cnv_line in mfile.readlines():
(chrid, start, end, cn, cov) = cnv_line.strip().split("\t")
expected_coverage = round((float(cn)*tumor_purity + 2*(1-tumor_purity)) * hap_coverage, 3)
wlines.append(cnv_line.strip() + "\t" + str(expected_coverage))
with open(out_file, "w") as ofile:
ofile.writelines("\n".join(wlines))
# Calculate expected coverage for each segment with shifted
cn_shift_suffix = []
if add_shift:
for cn_shift in [-2, -1, 1, 2]:
with open(merged_file, "r") as mfile:
wlines = ["#chr\tstart\tend\tCN\tobservedCoverage\texpectedCovearge"]
for cnv_line in mfile.readlines():
(chrid, start, end, cn, cov) = cnv_line.strip().split("\t")
expected_coverage = round(((float(cn) + cn_shift)*tumor_purity + 2*(1-tumor_purity)) * hap_coverage, 3)
wlines.append(cnv_line.strip() + "\t" + str(expected_coverage))
cn_shift_suffix.append("_CNshift_" + str(cn_shift))
with open(re.sub(".bed$", cn_shift_suffix[-1] + ".bed", out_file), "w") as ofile:
ofile.writelines("\n".join(wlines))
# Remove temporary files
if not save_tmp:
for rmf in rm_files:
print "rm %s" % os.path.join(out_dir, rmf)
subprocess.Popen("rm %s" % os.path.join(out_dir, rmf), shell=True)
print "Output bed file written"
if add_perc:
if os.path.basename(out_file)[:-4].endswith("_truth"):
sim_dir = "/illumina/scratch/tmp/users/ccolombo/simulation/" + os.path.basename(out_file)[4:-10]
else:
sim_dir = "/illumina/scratch/tmp/users/ccolombo/simulation/" + os.path.basename(out_file)[4:-4]
if os.path.exists(sim_dir):
# For each variant: clonal percentage, coverage of overlapping segments
perc_file = create_var_perc_file(sim_dir, None, True)
cmd = "/illumina/thirdparty/bedtools/bedtools2-2.22.1/bin/bedtools intersect"
cmd += " -a %s" % perc_file
cmd += " -b %s" % out_file
cmd += " -wa -wb"
run_bedtools_cmd(cmd, out_file, "_perc")
# For the whole genome: clonal percentage, coverage of overlapping bins
cmd = "/illumina/thirdparty/bedtools/bedtools2-2.22.1/bin/bedtools complement"
cmd += " -i %s" % perc_file
cmd += " -g %s" % hg_file
pc = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True)
compl = pc.stdout.readlines()
with open(perc_file, "r") as pbed:
lines = pbed.readlines()
for line in compl:
lines.append("\n" + line.rstrip() + "\t" + str(1) + "\t" + str(1) + "\t" + str(1.0))
with open(perc_file, "w") as pbed:
pbed.writelines(lines)
cmd = "/illumina/thirdparty/bedtools/bedtools2-2.22.1/bin/bedtools intersect"
cmd += " -a %s" % perc_file
cmd += " -b %s" % out_file_bin
cmd += " -wa -wb"
run_bedtools_cmd(cmd, out_file_bin, "_perc_all")
print("rm %s" % perc_file)
subprocess.Popen("rm %s" % perc_file, shell=True)
print "Output bed file with variants percentages written"
else:
print "Cannot find simulation directory"
def main():
"""Evaluate Canvas results on simulated data"""
parser = OptionParser()
parser.add_option(
"-s",
"--canvas_sim_id",
dest="canvas_sim_id",
type="string",
help=
"simulation id (find Canvas results directories strating with sim_id")
parser.add_option("-d",
"--canvas_sim_dir",
dest="canvas_sim_dir",
type="string",
help="Canvas results directory")
(options, args) = parser.parse_args()
if options.canvas_sim_dir is None and options.canvas_sim_id is None:
parser.error("Specify Canvas results simulation id or directory")
if options.canvas_sim_dir is not None and options.canvas_sim_id is not None:
parser.error(
"Canvas results simulation id and directory are mutually exclusive options"
)
if options.canvas_sim_dir is not None:
res_dirs = [options.canvas_sim_dir]
if options.canvas_sim_id is not None:
canvas_dir = "/illumina/scratch/tmp/users/ccolombo/Canvas/"
res_dirs = [
canvas_dir + cdir for cdir in os.listdir(canvas_dir)
if os.path.isdir((canvas_dir +
cdir)) and cdir.startswith(options.canvas_sim_id)
]
if len(res_dirs) == 0:
print "No Canvas results directories found"
hg_file = "/home/ccolombo/filtered_human.hg19.genome"
for res_dir in res_dirs:
print res_dir
sim_dir = re.sub("/Canvas/", "/simulation/", res_dir)
res_id = re.sub("sim", "ev", res_dir.split("/")[-1])
if not os.path.exists(res_dir):
print("\nCanvas results directory %s does not exist\n\n" % res_dir)
continue
if not os.path.exists(res_dir):
print("\nSimulation directory %s does not exist\n\n" % sim_dir)
continue
if os.path.basename(res_dir).startswith("simNorm") or res_dir.endswith(
"_purity100"):
continue
out_dir = os.path.join(
"/illumina/scratch/tmp/users/ccolombo/evaluation/EvaluateCNV",
res_id)
if not os.path.exists(out_dir):
os.mkdir(out_dir)
truth_file = create_het_cn_file(sim_dir,
os.path.join(out_dir,
"het_truth_file.bed"),
no_dipl=True,
hap_split=True,
round=True)
#truth_file = "/illumina/scratch/tmp/users/ccolombo/simulation/HCC2218flt.bed"
truth_file = add_BED_complement(truth_file,
hg_file,
sort=False,
out_dir=out_dir,
hap_split=True)
perc_file = create_var_perc_file(sim_dir,
os.path.join(out_dir, "var_perc.bed"),
no_dipl=True)
# Write simulation parameters to file
out_file = os.path.join(out_dir, res_id + "_par.txt")
if not os.path.exists(out_file):
get_sim_params(sim_dir, truth_file, perc_file, out_file, hg_file)
# Run EvaluateCNV
out_file = os.path.join(out_dir, res_id + ".txt")
excl_file = "/illumina/scratch/tmp/users/ccolombo/evaluation/sim_filter.bed"
if not os.path.exists(out_file):
#if True:
evaluate_CNV(res_dir, truth_file, excl_file, out_file)
# Run EvaluateCNV only on heterogeneous variants
out_file = os.path.join(out_dir, res_id + "_onlyhet.txt")
#if True:
if not os.path.exists(out_file):
with open(excl_file, "r") as ef:
excl_vars = ef.readlines()
with open(perc_file, "r") as pf:
for line in pf:
(chr_id, start, end, cnA, cnB,
perc) = line.strip().split("\t")
if float(perc) >= 0.8 and chr_id not in [
"chrX", "chrY", "chrM"
]:
excl_vars.append("\t".join([chr_id, start, end]) +
"\n")
os.system("rm %s" % (perc_file))
excl_file = os.path.join(out_dir, "filter_onlyhet.bed")
with open(excl_file, "w") as wf:
wf.writelines(excl_vars)
evaluate_CNV(res_dir, truth_file, excl_file, out_file)
