def run_age_single(intervals_bed=None, region_list=[], contig_dict={}, reference=None, assembly=None, pad=AGE_PAD,
age=None, truncation_pad_read_age = AGE_TRUNCATION_PAD,
max_interval_len_truncation_age = AGE_MAX_INTERVAL_TRUNCATION,
dist_to_expected_bp = AGE_DIST_TO_BP, min_del_subalign_len = MIN_DEL_SUBALIGN_LENGTH,
min_inv_subalign_len = MIN_INV_SUBALIGN_LENGTH, age_window = AGE_WINDOW_SIZE,
age_workdir=None, timeout=AGE_TIMEOUT, keep_temp=False, myid=0):
thread_logger = logging.getLogger("%s-%s" % (run_age_single.__name__, multiprocessing.current_process()))
bedtools_intervals = []
intervals_bedtool = pybedtools.BedTool(intervals_bed)
assembly_fasta = pysam.Fastafile(assembly) if assembly else None
reference_fasta = pysam.Fastafile(reference)
breakpoints_bed = None
thread_logger.info("Will process %d intervals" % (len(region_list)))
try:
for region in region_list:
bedtools_interval = pybedtools.Interval(region[0], region[1], region[3])
matching_intervals = [interval for interval in intervals_bedtool if (
interval.start == bedtools_interval.start and interval.end == bedtools_interval.end and interval.chrom == bedtools_interval.chrom)]
if not matching_intervals:
thread_logger.info("Matching interval not found for %s" % (str(bedtools_interval)))
matching_interval = bedtools_interval
else:
matching_interval = matching_intervals[0]
thread_logger.info("Matching interval %s" % (str(matching_interval)))
sc_locations = []
try:
sc_locations = map(int, json.loads(base64.b64decode(matching_interval.name.split(",")[0]))["SC_LOCATIONS"].split(","))
except:
pass
if region not in contig_dict:
continue
if not contig_dict[region]:
continue
region_object = SVRegion(region[0], region[1], region[2], region[3])
if region_object.pos1 - pad < 0:
thread_logger.error("Region too close to start of chromosome. Skipping.")
continue
reference_sequence = reference_fasta.fetch(reference=region_object.chrom1, start=region_object.pos1 - pad,
end=region_object.pos2 + pad)
region_name = "%s.%d.%d" % (region_object.chrom1, region_object.pos1, region_object.pos2)
ref_name = os.path.join(age_workdir, "%s.ref.fa" % region_name)
thread_logger.info("Writing the ref sequence for region %s" % region_name)
with open(ref_name, "w") as file_handle:
file_handle.write(">{}.ref\n{}".format(region_name, reference_sequence))
age_records = []
thread_logger.info("Processing %d contigs for region %s" % (len(contig_dict[region]), str(region_object)))
for contig in contig_dict[region]:
thread_logger.info(
"Writing the assembeled sequence %s of length %s" % (contig.raw_name, contig.sequence_len))
tr_region=[]
if region_object.length()>max_interval_len_truncation_age and contig.sv_type in ["INV","DEL","DUP"]:
# For large SVs, middle sequences has no effect on genotyping. So, we truncate middle region of reference to speed up
thread_logger.info("Truncate the reference sequence.")
truncate_start = pad + dist_to_expected_bp + truncation_pad_read_age +1
truncate_end = len(reference_sequence) - (pad + dist_to_expected_bp + truncation_pad_read_age)
reference_sequence_tr=reference_sequence[0:truncate_start-1]+reference_sequence[truncate_end:]
region_name_tr = "%s.%d.%d.tr_%d_%d" % (region_object.chrom1, region_object.pos1, region_object.pos2,truncate_start,truncate_end)
ref_name_tr = os.path.join(age_workdir, "%s.ref.fa" % region_name_tr)
thread_logger.info("Writing the truncated ref sequence for region %s, contig %s" % (region_name_tr, contig.raw_name))
with open(ref_name_tr, "w") as file_handle:
file_handle.write(">{}.ref\n{}".format(region_name_tr, reference_sequence_tr))
ref_len = len(reference_sequence_tr)
ref_f_name = ref_name_tr
tr_region = [truncate_start,truncate_end-truncate_start+1]
else:
ref_len = region_object.length()
ref_f_name = ref_name
if contig.sequence_len * ref_len >= 100000000:
thread_logger.info("Skipping contig because AGE problem is large (contig_len = %d , ref_len= %d)"%(contig.sequence_len, ref_len))
continue
contig_sequence = assembly_fasta.fetch(contig.raw_name)
prefix = get_age_file_prefix(contig)
asm_name = os.path.join(age_workdir, "%s.as.fa" % prefix)
out = os.path.join(age_workdir, "%s.age.out" % prefix)
err = os.path.join(age_workdir, "%s.age.err" % prefix)
fd_out = open(out, "w")
fd_err = open(err, "w")
with open(asm_name, "w") as file_handle:
file_handle.write(">{}.as\n{}".format(region_name, contig_sequence))
age_cmd = "%s %s -both -go=-6 %s %s" % (
age, "-inv" if contig.sv_type == "INV" else "-tdup" if contig.sv_type == "DUP" else "-indel",
ref_f_name, asm_name)
cmd_runner = TimedExternalCmd(age_cmd, thread_logger)
retcode = cmd_runner.run(timeout=timeout, cmd_log_fd_out=fd_out, cmd_log_fd_err=fd_err)
fd_out.close()
fd_err.close()
if retcode == 0:
age_record = AgeRecord(out,tr_region_1=tr_region)
if len(age_record.inputs) == 2:
age_record.contig = contig
age_record.set_assembly_contig(contig_sequence)
age_records.append(age_record)
else:
thread_logger.error("Number of inputs != 2 in age output file %s. Skipping." % out)
if not keep_temp:
os.remove(asm_name)
os.remove(err)
if tr_region:
os.remove(ref_name_tr)
unique_age_records = get_unique_age_records(age_records)
thread_logger.info("Unique %d AGE records for region %s" % (len(unique_age_records), str(region_object)))
for age_record in unique_age_records:
thread_logger.info(str(age_record))
sv_types = list(set([age_record.contig.sv_type for age_record in unique_age_records]))
if len(sv_types) != 1:
thread_logger.error("Some problem. Mixed SV types for this interval %s" % (str(sv_types)))
else:
sv_type = sv_types[0]
thread_logger.info("Processing region of type %s" % sv_type)
breakpoints, info_dict = process_age_records(unique_age_records, sv_type=sv_type,
pad=pad, dist_to_expected_bp=dist_to_expected_bp,
min_del_subalign_len=min_del_subalign_len,
min_inv_subalign_len=min_inv_subalign_len,
age_window=age_window, sc_locations=sc_locations)
bedtools_fields = matching_interval.fields
if len(breakpoints) == 1 and sv_type == "INS":
bedtools_fields += map(str, [breakpoints[0][0], breakpoints[0][0] + 1, breakpoints[0][1], breakpoints[0][2]])
elif len(breakpoints) == 2 and (sv_type in ["DEL","INV","DUP"]):
bedtools_fields += map(str, breakpoints + [breakpoints[1] - breakpoints[0]] + ["."])
else:
bedtools_fields += map(str, [bedtools_fields[1], bedtools_fields[2], -1, "."])
bedtools_fields[3] += ";AS"
bedtools_fields.append(base64.b64encode(json.dumps(info_dict)))
thread_logger.info("Writing out fields %s" % (str(bedtools_fields)))
bedtools_intervals.append(pybedtools.create_interval_from_list(bedtools_fields))
if not keep_temp:
os.remove(ref_name)
except Exception as e:
thread_logger.error('Caught exception in worker thread')
# This prints the type, value, and stack trace of the
# current exception being handled.
traceback.print_exc()
print()
raise e
if assembly_fasta:
assembly_fasta.close()
reference_fasta.close()
thread_logger.info("Writing %d intervals" % (len(bedtools_intervals)))
if bedtools_intervals:
breakpoints_bed = os.path.join(age_workdir, "%d_breakpoints.bed" % myid)
pybedtools.BedTool(bedtools_intervals).saveas(breakpoints_bed)
return breakpoints_bed
def run_age_single(intervals_bed=None, region_list=[], contig_dict={}, reference=None, assembly=None, pad=AGE_PAD,
age=None,
age_workdir=None, timeout=AGE_TIMEOUT, keep_temp=False, myid=0):
thread_logger = logging.getLogger("%s-%s" % (run_age_single.__name__, multiprocessing.current_process()))
bedtools_intervals = []
intervals_bedtool = pybedtools.BedTool(intervals_bed)
assembly_fasta = pysam.Fastafile(assembly) if assembly else None
reference_fasta = pysam.Fastafile(reference)
breakpoints_bed = None
thread_logger.info("Will process %d intervals" % (len(region_list)))
try:
for region in region_list:
bedtools_interval = pybedtools.Interval(region[0], region[1], region[3])
matching_intervals = [interval for interval in intervals_bedtool if (
interval.start == bedtools_interval.start and interval.end == bedtools_interval.end and interval.chrom == bedtools_interval.chrom)]
if not matching_intervals:
thread_logger.info("Matching interval not found for %s" % (str(bedtools_interval)))
matching_interval = bedtools_interval
else:
matching_interval = matching_intervals[0]
thread_logger.info("Matching interval %s" % (str(matching_interval)))
if region not in contig_dict:
continue
if not contig_dict[region]:
continue
region_object = SVRegion(region[0], region[1], region[2], region[3])
if region_object.pos1 - pad < 0:
thread_logger.error("Region too close to start of chromosome. Skipping.")
continue
reference_sequence = reference_fasta.fetch(reference=region_object.chrom1, start=region_object.pos1 - pad,
end=region_object.pos2 + pad)
region_name = "%s.%d.%d" % (region_object.chrom1, region_object.pos1, region_object.pos2)
ref_name = os.path.join(age_workdir, "%s.ref.fa" % region_name)
thread_logger.info("Writing the ref sequence for region %s" % region_name)
with open(ref_name, "w") as file_handle:
file_handle.write(">{}.ref\n{}".format(region_name, reference_sequence))
age_records = []
thread_logger.info("Processing %d contigs for region %s" % (len(contig_dict[region]), str(region_object)))
for contig in contig_dict[region]:
thread_logger.info(
"Writing the assembeled sequence %s of length %s" % (contig.raw_name, contig.sequence_len))
if contig.sequence_len * region_object.length() >= 100000000:
thread_logger.info("Skipping contig because AGE problem is large")
continue
contig_sequence = assembly_fasta.fetch(contig.raw_name)
prefix = get_age_file_prefix(contig)
asm_name = os.path.join(age_workdir, "%s.as.fa" % prefix)
out = os.path.join(age_workdir, "%s.age.out" % prefix)
err = os.path.join(age_workdir, "%s.age.err" % prefix)
with open(asm_name, "w") as file_handle:
file_handle.write(">{}.as\n{}".format(region_name, contig_sequence))
age_cmd = "%s %s -both -go=-6 %s %s >%s 2>%s" % (
age,
"-inv" if contig.sv_type == "INV" else "-indel",
ref_name,
asm_name,
out,
err)
execute_cmd = "timeout %ds %s" % (timeout, age_cmd)
retcode = run_cmd(execute_cmd, thread_logger, None, None)
if retcode == 0:
age_record = AgeRecord(out)
if len(age_record.inputs) == 2:
age_record.contig = contig
age_records.append(age_record)
else:
thread_logger.error("Number of inputs != 2 in age output file %s. Skipping." % out)
if not keep_temp:
os.remove(asm_name)
os.remove(err)
unique_age_records = get_unique_age_records(age_records)
thread_logger.info("Unique %d AGE records for region %s" % (len(unique_age_records), str(region_object)))
for age_record in unique_age_records:
thread_logger.info(str(age_record))
sv_types = list(set([age_record.contig.sv_type for age_record in unique_age_records]))
if len(sv_types) != 1:
thread_logger.error("Some problem. Mixed SV types for this interval %s" % (str(sv_types)))
else:
sv_type = sv_types[0]
thread_logger.info("Processing region of type %s" % sv_type)
breakpoints, info_dict = process_age_records(unique_age_records, sv_type=sv_type, pad=pad)
bedtools_fields = matching_interval.fields
if len(breakpoints) == 1 and sv_type == "INS":
bedtools_fields += map(str, [breakpoints[0][0], breakpoints[0][0] + 1, breakpoints[0][1]])
elif len(breakpoints) == 2 and (sv_type == "DEL" or sv_type == "INV"):
bedtools_fields += map(str, breakpoints + [breakpoints[1] - breakpoints[0]])
else:
bedtools_fields += map(str, [bedtools_fields[1], bedtools_fields[2], -1])
bedtools_fields.append(base64.b64encode(json.dumps(info_dict)))
thread_logger.info("Writing out fields %s" % (str(bedtools_fields)))
bedtools_intervals.append(pybedtools.create_interval_from_list(bedtools_fields))
if not keep_temp:
os.remove(ref_name)
except Exception as e:
thread_logger.error('Caught exception in worker thread')
# This prints the type, value, and stack trace of the
# current exception being handled.
traceback.print_exc()
print()
raise e
if assembly_fasta:
assembly_fasta.close()
reference_fasta.close()
thread_logger.info("Writing %d intervals" % (len(bedtools_intervals)))
if bedtools_intervals:
breakpoints_bed = os.path.join(age_workdir, "%d_breakpoints.bed" % myid)
pybedtools.BedTool(bedtools_intervals).saveas(breakpoints_bed)
return breakpoints_bed
def run_age_single(intervals_bed=None,
region_list=[],
contig_dict={},
reference=None,
assembly=None,
pad=AGE_PAD,
age=None,
truncation_pad_read_age=AGE_TRUNCATION_PAD,
max_interval_len_truncation_age=AGE_MAX_INTERVAL_TRUNCATION,
dist_to_expected_bp=AGE_DIST_TO_BP,
min_del_subalign_len=MIN_DEL_SUBALIGN_LENGTH,
min_inv_subalign_len=MIN_INV_SUBALIGN_LENGTH,
age_window=AGE_WINDOW_SIZE,
age_workdir=None,
timeout=AGE_TIMEOUT,
keep_temp=False,
myid=0):
thread_logger = logging.getLogger(
"%s-%s" % (run_age_single.__name__, multiprocessing.current_process()))
bedtools_intervals = []
intervals_bedtool = pybedtools.BedTool(intervals_bed)
assembly_fasta = pysam.Fastafile(assembly) if assembly else None
reference_fasta = pysam.Fastafile(reference)
breakpoints_bed = None
thread_logger.info("Will process %d intervals" % (len(region_list)))
try:
for region in region_list:
bedtools_interval = pybedtools.Interval(region[0], region[1],
region[3])
matching_intervals = [
interval for interval in intervals_bedtool
if (interval.start == bedtools_interval.start
and interval.end == bedtools_interval.end
and interval.chrom == bedtools_interval.chrom)
]
if not matching_intervals:
thread_logger.info("Matching interval not found for %s" %
(str(bedtools_interval)))
matching_interval = bedtools_interval
else:
matching_interval = matching_intervals[0]
thread_logger.info("Matching interval %s" %
(str(matching_interval)))
sc_locations = []
try:
sc_locations = map(
int,
json.loads(
base64.b64decode(matching_interval.name.split(",")[0]))
["SC_LOCATIONS"].split(","))
except:
pass
if region not in contig_dict:
continue
if not contig_dict[region]:
continue
region_object = SVRegion(region[0], region[1], region[2],
region[3])
if region_object.pos1 - pad < 0:
thread_logger.error(
"Region too close to start of chromosome. Skipping.")
continue
reference_sequence = reference_fasta.fetch(
reference=region_object.chrom1,
start=region_object.pos1 - pad,
end=region_object.pos2 + pad)
region_name = "%s.%d.%d" % (region_object.chrom1,
region_object.pos1, region_object.pos2)
ref_name = os.path.join(age_workdir, "%s.ref.fa" % region_name)
thread_logger.info("Writing the ref sequence for region %s" %
region_name)
with open(ref_name, "w") as file_handle:
file_handle.write(">{}.ref\n{}".format(region_name,
reference_sequence))
age_records = []
thread_logger.info("Processing %d contigs for region %s" %
(len(contig_dict[region]), str(region_object)))
for contig in contig_dict[region]:
thread_logger.info(
"Writing the assembeled sequence %s of length %s" %
(contig.raw_name, contig.sequence_len))
tr_region = []
if region_object.length(
) > max_interval_len_truncation_age and contig.sv_type in [
"INV", "DEL", "DUP"
]:
# For large SVs, middle sequences has no effect on genotyping. So, we truncate middle region of reference to speed up
thread_logger.info("Truncate the reference sequence.")
truncate_start = pad + dist_to_expected_bp + truncation_pad_read_age + 1
truncate_end = len(reference_sequence) - (
pad + dist_to_expected_bp + truncation_pad_read_age)
reference_sequence_tr = reference_sequence[
0:truncate_start -
1] + reference_sequence[truncate_end:]
region_name_tr = "%s.%d.%d.tr_%d_%d" % (
region_object.chrom1, region_object.pos1,
region_object.pos2, truncate_start, truncate_end)
ref_name_tr = os.path.join(age_workdir,
"%s.ref.fa" % region_name_tr)
thread_logger.info(
"Writing the truncated ref sequence for region %s, contig %s"
% (region_name_tr, contig.raw_name))
with open(ref_name_tr, "w") as file_handle:
file_handle.write(">{}.ref\n{}".format(
region_name_tr, reference_sequence_tr))
ref_len = len(reference_sequence_tr)
ref_f_name = ref_name_tr
tr_region = [
truncate_start, truncate_end - truncate_start + 1
]
else:
ref_len = region_object.length()
ref_f_name = ref_name
if contig.sequence_len * ref_len >= 100000000:
thread_logger.info(
"Skipping contig because AGE problem is large (contig_len = %d , ref_len= %d)"
% (contig.sequence_len, ref_len))
continue
contig_sequence = assembly_fasta.fetch(contig.raw_name)
prefix = get_age_file_prefix(contig)
asm_name = os.path.join(age_workdir, "%s.as.fa" % prefix)
out = os.path.join(age_workdir, "%s.age.out" % prefix)
err = os.path.join(age_workdir, "%s.age.err" % prefix)
fd_out = open(out, "w")
fd_err = open(err, "w")
with open(asm_name, "w") as file_handle:
file_handle.write(">{}.as\n{}".format(
region_name, contig_sequence))
age_cmd = "%s %s -both -go=-6 %s %s" % (
age, "-inv" if contig.sv_type == "INV" else
"-tdup" if contig.sv_type == "DUP" else "-indel",
ref_f_name, asm_name)
cmd_runner = TimedExternalCmd(age_cmd, thread_logger)
retcode = cmd_runner.run(timeout=timeout,
cmd_log_fd_out=fd_out,
cmd_log_fd_err=fd_err)
fd_out.close()
fd_err.close()
if retcode == 0:
age_record = AgeRecord(out, tr_region_1=tr_region)
if len(age_record.inputs) == 2:
age_record.contig = contig
age_record.set_assembly_contig(contig_sequence)
age_records.append(age_record)
else:
thread_logger.error(
"Number of inputs != 2 in age output file %s. Skipping."
% out)
if not keep_temp:
os.remove(asm_name)
os.remove(err)
if tr_region:
os.remove(ref_name_tr)
unique_age_records = get_unique_age_records(age_records)
thread_logger.info("Unique %d AGE records for region %s" %
(len(unique_age_records), str(region_object)))
for age_record in unique_age_records:
thread_logger.info(str(age_record))
sv_types = list(
set([
age_record.contig.sv_type
for age_record in unique_age_records
]))
if len(sv_types) != 1:
thread_logger.error(
"Some problem. Mixed SV types for this interval %s" %
(str(sv_types)))
else:
sv_type = sv_types[0]
thread_logger.info("Processing region of type %s" % sv_type)
breakpoints, info_dict = process_age_records(
unique_age_records,
sv_type=sv_type,
pad=pad,
dist_to_expected_bp=dist_to_expected_bp,
min_del_subalign_len=min_del_subalign_len,
min_inv_subalign_len=min_inv_subalign_len,
age_window=age_window,
sc_locations=sc_locations)
bedtools_fields = matching_interval.fields
if len(breakpoints) == 1 and sv_type == "INS":
bedtools_fields += map(str, [
breakpoints[0][0], breakpoints[0][0] + 1,
breakpoints[0][1], breakpoints[0][2]
])
elif len(breakpoints) == 2 and (sv_type
in ["DEL", "INV", "DUP"]):
bedtools_fields += map(
str, breakpoints + [breakpoints[1] - breakpoints[0]] +
["."])
else:
bedtools_fields += map(
str, [bedtools_fields[1], bedtools_fields[2], -1, "."])
bedtools_fields[3] += ";AS"
bedtools_fields.append(base64.b64encode(json.dumps(info_dict)))
thread_logger.info("Writing out fields %s" %
(str(bedtools_fields)))
bedtools_intervals.append(
pybedtools.create_interval_from_list(bedtools_fields))
if not keep_temp:
os.remove(ref_name)
except Exception as e:
thread_logger.error('Caught exception in worker thread')
# This prints the type, value, and stack trace of the
# current exception being handled.
traceback.print_exc()
print()
raise e
if assembly_fasta:
assembly_fasta.close()
reference_fasta.close()
thread_logger.info("Writing %d intervals" % (len(bedtools_intervals)))
if bedtools_intervals:
breakpoints_bed = os.path.join(age_workdir,
"%d_breakpoints.bed" % myid)
pybedtools.BedTool(bedtools_intervals).saveas(breakpoints_bed)
return breakpoints_bed
def run_age_single(intervals_bed=None,
region_list=[],
contig_dict={},
reference=None,
assembly=None,
pad=AGE_PAD,
age=None,
age_workdir=None,
timeout=AGE_TIMEOUT,
keep_temp=False,
myid=0):
thread_logger = logging.getLogger(
"%s-%s" % (run_age_single.__name__, multiprocessing.current_process()))
bedtools_intervals = []
intervals_bedtool = pybedtools.BedTool(intervals_bed)
assembly_fasta = pysam.Fastafile(assembly)
reference_fasta = pysam.Fastafile(reference)
breakpoints_bed = None
thread_logger.info("Will process %d intervals" % (len(region_list)))
try:
for region in region_list:
bedtools_interval = pybedtools.Interval(region[0], region[1],
region[3])
matching_intervals = [
interval for interval in intervals_bedtool
if (interval.start == bedtools_interval.start
and interval.end == bedtools_interval.end
and interval.chrom == bedtools_interval.chrom)
]
if not matching_intervals:
thread_logger.info("Matching interval not found for %s" %
(str(bedtools_interval)))
matching_interval = bedtools_interval
else:
matching_interval = matching_intervals[0]
thread_logger.info("Matching interval %s" %
(str(matching_interval)))
if region not in contig_dict:
continue
if not contig_dict[region]:
continue
region_object = SVRegion(region[0], region[1], region[2],
region[3])
if region_object.pos1 - pad < 0:
thread_logger.error(
"Region too close to start of chromosome. Skipping.")
continue
reference_sequence = reference_fasta.fetch(
reference=region_object.chrom1,
start=region_object.pos1 - pad,
end=region_object.pos2 + pad)
region_name = "%s.%d.%d" % (region_object.chrom1,
region_object.pos1, region_object.pos2)
ref_name = os.path.join(age_workdir, "%s.ref.fa" % region_name)
thread_logger.info("Writing the ref sequence for region %s" %
region_name)
with open(ref_name, "w") as file_handle:
file_handle.write(">{}.ref\n{}".format(region_name,
reference_sequence))
age_records = []
thread_logger.info("Processing %d contigs for region %s" %
(len(contig_dict[region]), str(region_object)))
for contig in contig_dict[region]:
thread_logger.info(
"Writing the assembeled sequence %s of length %s" %
(contig.raw_name, contig.sequence_len))
if contig.sequence_len * region_object.length() >= 100000000:
thread_logger.info(
"Skipping contig because AGE problem is large")
continue
contig_sequence = assembly_fasta.fetch(contig.raw_name)
prefix = get_age_file_prefix(contig)
asm_name = os.path.join(age_workdir, "%s.as.fa" % prefix)
out = os.path.join(age_workdir, "%s.age.out" % prefix)
err = os.path.join(age_workdir, "%s.age.err" % prefix)
with open(asm_name, "w") as file_handle:
file_handle.write(">{}.as\n{}".format(
region_name, contig_sequence))
age_cmd = "%s %s -both -go=-6 %s %s >%s 2>%s" % (
age, "-inv" if contig.sv_type == "INV" else "-indel",
ref_name, asm_name, out, err)
execute_cmd = "timeout %ds %s" % (timeout, age_cmd)
retcode = run_cmd(execute_cmd, thread_logger, None, None)
if retcode == 0:
age_record = AgeRecord(out)
if len(age_record.inputs) == 2:
age_record.contig = contig
age_records.append(age_record)
else:
thread_logger.error(
"Number of inputs != 2 in age output file %s. Skipping."
% out)
if not keep_temp:
os.remove(asm_name)
os.remove(err)
unique_age_records = get_unique_age_records(age_records)
thread_logger.info("Unique %d AGE records for region %s" %
(len(unique_age_records), str(region_object)))
for age_record in unique_age_records:
thread_logger.info(str(age_record))
sv_types = list(
set([
age_record.contig.sv_type
for age_record in unique_age_records
]))
if len(sv_types) != 1:
thread_logger.error(
"Some problem. Mixed SV types for this interval %s" %
(str(sv_types)))
else:
sv_type = sv_types[0]
thread_logger.info("Processing region of type %s" % sv_type)
breakpoints, info_dict = process_age_records(
unique_age_records, sv_type=sv_type, pad=pad)
bedtools_fields = matching_interval.fields
if len(breakpoints) == 1 and sv_type == "INS":
bedtools_fields += map(str, [
breakpoints[0][0], breakpoints[0][0] + 1,
breakpoints[0][1]
])
elif len(breakpoints) == 2 and (sv_type == "DEL"
or sv_type == "INV"):
bedtools_fields += map(
str, breakpoints + [breakpoints[1] - breakpoints[0]])
else:
bedtools_fields += map(
str, [bedtools_fields[1], bedtools_fields[2], -1])
bedtools_fields.append(base64.b64encode(json.dumps(info_dict)))
thread_logger.info("Writing out fields %s" %
(str(bedtools_fields)))
bedtools_intervals.append(
pybedtools.create_interval_from_list(bedtools_fields))
if not keep_temp:
os.remove(ref_name)
except Exception as e:
thread_logger.error('Caught exception in worker thread')
# This prints the type, value, and stack trace of the
# current exception being handled.
traceback.print_exc()
print()
raise e
assembly_fasta.close()
reference_fasta.close()
thread_logger.info("Writing %d intervals" % (len(bedtools_intervals)))
if bedtools_intervals:
breakpoints_bed = os.path.join(age_workdir,
"%d_breakpoints.bed" % myid)
pybedtools.BedTool(bedtools_intervals).saveas(breakpoints_bed)
return breakpoints_bed
