def __init__(self, chromosome_name, bam_file_path, draft_file_path,
truth_bam, train_mode):
"""
Initialize a manager object
:param chromosome_name: Name of the chromosome
:param bam_file_path: Path to the BAM file
:param draft_file_path: Path to the reference FASTA file
:param truth_bam: Path to the truth sequence to reference mapping file
"""
# --- initialize handlers ---
# create objects to handle different files and query
self.bam_path = bam_file_path
self.fasta_path = draft_file_path
self.bam_handler = PEPPER.BAM_handler(bam_file_path)
self.fasta_handler = PEPPER.FASTA_handler(draft_file_path)
self.train_mode = train_mode
self.downsample_rate = 1.0
self.truth_bam_handler = None
if self.train_mode:
self.truth_bam_handler = PEPPER.BAM_handler(truth_bam)
# --- initialize names ---
# name of the chromosome
self.chromosome_name = chromosome_name
def get_chromosome_list(chromosome_names, ref_file, bam_file, region_bed):
"""
PARSES THROUGH THE CHROMOSOME PARAMETER TO FIND OUT WHICH REGIONS TO PROCESS
:param chromosome_names: NAME OF CHROMOSOME
:param ref_file: PATH TO THE REFERENCE FILE
:param bam_file: PATH TO BAM FILE
:return: LIST OF CHROMOSOME IN REGION SPECIFIC FORMAT
"""
if not chromosome_names and not region_bed:
fasta_handler = PEPPER.FASTA_handler(ref_file)
bam_handler = PEPPER.BAM_handler(bam_file)
bam_contigs = bam_handler.get_chromosome_sequence_names()
fasta_contigs = fasta_handler.get_chromosome_names()
common_contigs = list(set(fasta_contigs) & set(bam_contigs))
if len(common_contigs) == 0:
sys.stderr.write(
"[" + datetime.now().strftime('%m-%d-%Y %H:%M:%S') + "] " +
"ERROR: NO COMMON CONTIGS FOUND BETWEEN THE BAM FILE AND THE FASTA FILE."
)
sys.stderr.flush()
exit(1)
common_contigs = sorted(common_contigs,
key=UserInterfaceSupport.natural_key)
sys.stderr.write("[" +
datetime.now().strftime('%m-%d-%Y %H:%M:%S') +
"] INFO: COMMON CONTIGS FOUND: " +
str(common_contigs) + "\n")
sys.stderr.flush()
chromosome_name_list = []
for contig_name in common_contigs:
chromosome_name_list.append((contig_name, None))
return chromosome_name_list
if region_bed:
chromosome_name_list = []
with open(region_bed) as fp:
line = fp.readline()
cnt = 1
while line:
line_to_list = line.rstrip().split('\t')
chr_name, start_pos, end_pos = line_to_list[0], int(
line_to_list[1]), int(line_to_list[2])
region = sorted([start_pos, end_pos])
chromosome_name_list.append((chr_name, region))
line = fp.readline()
cnt += 1
return chromosome_name_list
split_names = chromosome_names.strip().split(',')
split_names = [name.strip() for name in split_names]
chromosome_name_list = []
for name in split_names:
# split on region
region = None
if ':' in name:
name_region = name.strip().split(':')
if len(name_region) != 2:
sys.stderr.write("ERROR: --region INVALID value.\n")
exit(0)
name, region = tuple(name_region)
region = region.strip().split('-')
region = [int(pos) for pos in region]
if len(region) != 2 or not region[0] <= region[1]:
sys.stderr.write("ERROR: --region INVALID value.\n")
exit(0)
range_split = name.split('-')
if len(range_split) > 1:
chr_prefix = ''
for p in name:
if p.isdigit():
break
else:
chr_prefix = chr_prefix + p
int_ranges = []
for item in range_split:
s = ''.join(i for i in item if i.isdigit())
int_ranges.append(int(s))
int_ranges = sorted(int_ranges)
for chr_seq in range(int_ranges[0], int_ranges[-1] + 1):
chromosome_name_list.append(
(chr_prefix + str(chr_seq), region))
else:
chromosome_name_list.append((name, region))
return chromosome_name_list
def chromosome_level_parallelization(chr_list, bam_file, draft_file,
truth_bam, output_path, total_threads,
train_mode):
if train_mode:
max_size = 1000
else:
max_size = 1000
start_time = time.time()
fasta_handler = PEPPER.FASTA_handler(draft_file)
contigs = set()
all_intervals = []
# first calculate all the intervals that we need to process
for chr_name, region in chr_list:
# contig update message
contigs.add(str(chr_name))
if not region:
interval_start, interval_end = (
0,
fasta_handler.get_chromosome_sequence_length(
str(chr_name)) - 1)
else:
interval_start, interval_end = tuple(region)
interval_start = max(0, interval_start)
interval_end = min(
interval_end,
fasta_handler.get_chromosome_sequence_length(str(chr_name))
- 1)
# this is the interval size each of the process is going to get which is 10^6
# I will split this into 10^4 size inside the worker process
for pos in range(interval_start, interval_end, max_size):
pos_start = max(interval_start,
pos - ImageSizeOptions.MIN_IMAGE_OVERLAP)
pos_end = min(
interval_end,
pos + max_size + ImageSizeOptions.MIN_IMAGE_OVERLAP)
all_intervals.append((chr_name, pos_start, pos_end))
# all intervals calculated now
# contig update message
sys.stderr.write("[" + datetime.now().strftime('%m-%d-%Y %H:%M:%S') +
"] " + "INFO: TOTAL CONTIGS: " + str(len(contigs)) +
" TOTAL INTERVALS: " + str(len(all_intervals)) + "\n")
sys.stderr.flush()
args = (output_path, bam_file, draft_file, truth_bam, train_mode)
with concurrent.futures.ProcessPoolExecutor(
max_workers=total_threads) as executor:
futures = [
executor.submit(UserInterfaceSupport.image_generator, args,
all_intervals, total_threads, thread_id)
for thread_id in range(0, total_threads)
]
for fut in concurrent.futures.as_completed(futures):
if fut.exception() is None:
# get the results
thread_id = fut.result()
sys.stderr.write(
"[" + datetime.now().strftime('%m-%d-%Y %H:%M:%S') +
"] " + "INFO: THREAD " + str(thread_id) +
" FINISHED SUCCESSFULLY.\n")
else:
sys.stderr.write(
"[" +
str(datetime.now().strftime('%m-%d-%Y %H:%M:%S')) +
"] ERROR: " + str(fut.exception()) + "\n")
fut._result = None # python issue 27144
end_time = time.time()
mins = int((end_time - start_time) / 60)
secs = int((end_time - start_time)) % 60
sys.stderr.write("[" +
str(datetime.now().strftime('%m-%d-%Y %H:%M:%S')) +
"] INFO: FINISHED IMAGE GENERATION\n")
sys.stderr.write("[" +
str(datetime.now().strftime('%m-%d-%Y %H:%M:%S')) +
"] INFO: ELAPSED TIME: " + str(mins) + " Min " +
str(secs) + " Sec\n")