other_type_calls += 1
continue
calls_gte_threshold.append(line)
bed_lines = []
for line in calls_gte_threshold:
fields = line.split("\t")
# need to strip off the "chr"
chrom = fields[1][3:len(fields[1])]
if (int(fields[2]) > int(fields[3])):
sys.stderr.write("warning, start is greater than end: " + "\t".join([chrom, fields[2], fields[3]]) + "\n")
continue
if (sv_type == "DEL"):
bed_line = "\t".join([chrom, fields[2], fields[3]])
else:
bed_line = "\t".join([chrom, fields[2], fields[3], str(abs(int(float(fields[6]))))])
bed_lines.append(bed_line)
if print_bed:
print "\n".join(bed_lines)
sys.exit(0)
if (sv_type == "DEL"):
(qualified_calls, matches, short_calls) = evalBedFile.eval_bed_deletions(truth_filename, bed_lines, print_hits)
else:
(qualified_calls, matches, short_calls) = evalBedFile.eval_bed_insertions(truth_filename, bed_lines, print_hits)
tpr = float(matches) / (qualified_calls)
if not print_hits:
print "\t".join(map(str, [v, qualified_calls, matches, other_type_calls, short_calls, tpr]))
pindel_file = open(pindel_long_insertions_filename, "r")
for line in pindel_file:
fields = line.split()
if len(fields) < 2 or fields[1] != "LI":
continue
if float(fields[6]) * float(fields[9]) >= v:
chrom = fields[3]
ostart = fields[4]
oend = fields[7]
length = "100"
bed_line = "\t".join([chrom, ostart, oend, length])
#print bed_line.strip()
calls_gte_threshold.append(bed_line)
pindel_file.close()
if print_bed:
print "\n".join(calls_gte_threshold)
continue
if sv_type == "DEL":
(qualified_calls, matches, short_calls) = evalBedFile.eval_bed_deletions(truth_filename, calls_gte_threshold, print_hits)
else:
(qualified_calls, matches, short_calls) = evalBedFile.eval_bed_insertions(truth_filename, calls_gte_threshold, print_hits)
if (qualified_calls > 0):
tpr = float(matches) / (qualified_calls)
else:
tpr = "NA"
if not print_hits:
print "\t".join(map(str, [v, qualified_calls, matches, 0, short_calls, tpr]))