def init_file_names(chr, event,tmpbams_path, haplotypedir):
flist=[]
splitbams = params.GetSplitBamsPath()
roibam = "/".join([tmpbams_path ,chr + event +"_roi.bam"])
sortbyname = "/".join([splitbams, chr + '.byname.bam'])
sortbyCoord = "/".join([splitbams, chr + '.bam'])
hetsnp = "/".join([haplotypedir, event+'_het_snp_' + chr + '.bed'])
flist.extend([roibam,sortbyname,sortbyCoord,hetsnp])
return flist
def find_non_roi_bam(chr_list):
"""
Extract paired reads from original bam using generated non-ROI bed.
"""
chr = chr_list
splitbams = params.GetSplitBamsPath()
sortbyname = "/".join([splitbams, chr + '.byname.bam'])
sortbyCoord = "/".join([splitbams, chr + '.bam'])
nonroi = "/".join([finalbams_path, chr + "_non_roi.bam"])
exonsnonroibed = "/".join([haplotype_path, chr + "_non_roi.bed"])
success = False
try:
if not terminating.is_set():
nonroisort = sub('.bam$', '.sorted', nonroi)
if os.path.isfile(nonroisort):
success = True
else:
if os.path.isfile(exonsnonroibed):
cmd = " ".join(["sort -u", exonsnonroibed, "-o", exonsnonroibed]);
runCommand(cmd)
print(" ___ extracting non-roi bams ___")
extractAllReadsfromROI(sortbyCoord, exonsnonroibed, nonroi)
removeIfEmpty(finalbams_path, ntpath.basename(nonroi))
pysam.sort(nonroi, nonroisort)
pysam.index(nonroisort + '.bam')
os.remove(nonroi)
success = True
else:
logger.debug(exonsnonroibed + ' does not exist!')
return
except (KeyboardInterrupt):
logger.error('Exception Crtl+C pressed in the child process in find_roi_bam for chr ' + chr)
terminating.set()
success = False
return
except Exception as e:
logger.exception("Exception in find_non_roi_bam %s", e)
terminating.set()
success = False
return
if (success):
logger.debug("find_non_roi_bam complete successfully for " + chr)
return
def init_file_names(chr, tmpbams_path, haplotypedir, event=''):
flist = []
roibam = "/".join([tmpbams_path, chr + "_roi" + event + ".bam"])
splitbams = params.GetSplitBamsPath()
hetsnp = "/".join([haplotypedir, chr + '_het_snp' + event + '.bed'])
if (not splitbams):
splitbams = "/".join([res_path, 'splitbams'])
sortbyname = "/".join([splitbams, chr + '.byname.bam'])
sortbyCoord = "/".join([splitbams, chr + '.bam'])
flist.extend([roibam, sortbyname, sortbyCoord, hetsnp])
return flist
def mergeSortBamFiles(mergedBamfn, finalbamdir):
java_path, beagle_path, samtools_path, bedtools_path, vcftools_path, sambamba_path = params.GetSoftwarePath(
)
command = ""
os.chdir(finalbamdir)
matches = []
num_files = 0
for root, dirnames, filenames in os.walk(finalbamdir):
for filename in fnmatch.filter(filenames, '*.bam'):
path = os.path.join(root, filename)
if os.path.islink(path):
path = os.path.realpath(path)
if not matches.__contains__(path):
matches.append(path)
command = " ".join([path, command])
num_files = num_files + 1
if num_files > 1:
command2 = " ".join([
sambamba_path, "merge", mergedBamfn, command, "--nthreads",
str(4)
])
runCommand(command2)
elif num_files == 1:
if str(command.strip()).endswith("GAIN.bam"):
path, fname = os.path.split(str(command.strip()))
inbam_original = '/'.join(
[params.GetSplitBamsPath(),
sub('_gain', '', fname.lower())])
command2 = " ".join([
sambamba_path, "merge", mergedBamfn, command, inbam_original,
"--nthreads",
str(4)
])
runCommand(command2)
elif str(command.strip()).endswith("LOSS.bam"):
outbam = sub('.bam$', '.sort.bam', str(command.strip()))
sortBam(command, outbam, finalbamdir)
os.remove(str(command.strip()))
def init_file_names(chr, tmpbams_path, haplotypedir, event):
"""
Initialize file names for:
ROI bam, chromosome sorted by name, chromosome sorted by coordinate, and heterozygous SNPs bed.
"""
flist = []
roibam = "/".join([tmpbams_path, chr + "_roi" + event + ".bam"])
splitbams = params.GetSplitBamsPath()
hetsnp = "/".join([haplotypedir, chr + '_het_snp' + event + '.bed'])
if not splitbams:
splitbams = "/".join([res_path, 'splitbams'])
sortbyname = "/".join([splitbams, chr + '.byname.bam'])
sortbyCoord = "/".join([splitbams, chr + '.bam'])
flist.extend([roibam, sortbyname, sortbyCoord, hetsnp])
return flist
def CreateFileList(file_type, num_files, path, flag=None):
sentinel_path, results_path, haplotype_path, cancer_dir_path, tmpbams_path, finalbams_path = GetProjectNamePathRunID(
)
job_list = []
infile_list = ParseInfile(params.GetInfile())
for line in infile_list:
file_list = []
job_info = line
## Find the tumour_id for the sample
sample_id = GetSampleIDs(line)
if (flag is None):
if file_type == 'bam':
file_list.append(line[1])
elif num_files == 1:
file_list.append(path + file_type.format(sample_id))
elif num_files >= 2:
for chr in chr_list:
file_list.append(path + file_type.format('chr', str(chr)))
else:
file_list.append('')
job_list.append(file_list)
elif (flag == "extractROI"):
for chr, event in itertools.product(chr_list, event_list):
exonsinroibed = "/".join([
haplotype_path,
event + "_exons_in_roi_" + 'chr' + str(chr) + '.bed'
])
if (os.path.isfile(exonsinroibed)):
splittmpbams = "/".join([path])
file_list.append(splittmpbams + '/' + 'chr' +
file_type.format(chr, event))
job_list.append(file_list)
elif (flag == "gain"):
for chr in chr_list:
splittmpbams = "/".join([path])
if (os.path.isfile(splittmpbams + '/' + 'chr' + str(chr) +
'.gain.roi.sorted.bam')):
file_list.append(splittmpbams + '/' + 'chr' +
file_type.format(chr, "gain"))
job_list.append(file_list)
elif (flag == "loss"):
for chr in chr_list:
splittmpbams = "/".join([path])
if (os.path.isfile(splittmpbams + '/' + 'chr' + str(chr) +
'.loss.roi.sorted.bam')):
file_list.append(splittmpbams + '/' + 'chr' +
file_type.format(chr, "loss"))
job_list.append(file_list)
elif (flag == "FINAL"):
for chr, event in itertools.product(chr_list, event_list):
chrbam = "/".join([
finalbams_path,
'CHR' + str(chr) + '_' + event.upper() + '.bam'
])
sortbyCoord = "/".join(
[params.GetSplitBamsPath(), 'chr' + str(chr) + '.bam'])
if (os.path.isfile(chrbam)):
file_list.append(chrbam)
job_list.append(file_list)
elif (event == 'loss' and sortbyCoord):
os.symlink(sortbyCoord, chrbam)
return job_list
def run_pipeline(results_path):
print(results_path)
global haplotype_path, cancer_dir_path, tmpbams_path, finalbams_path, log_path, logfile, terminating, logger, logQueue, res_path
res_path = results_path
haplotype_path, cancer_dir_path, tmpbams_path, finalbams_path, log_path, logfile = handle.GetProjectPaths(
results_path)
terminating, logger, logQueue = handle.GetLoggings(logfile)
chr_list = ['chr' + str(x) for x in range(1, 23)]
chr_list.extend(['chrX', 'chrY'])
t0 = time.time()
outbamfn = params.GetOutputFileName()
cnv_list = glob.glob("/".join([params.GetCNVDir(), '*.*']))
chromosome_event = create_chr_event_list(cnv_list, chr_list)
logger.debug('pipeline started!')
phase_path = '/'.join([results_path, 'phasedvcfdir'])
if not os.path.exists('/'.join([results_path, 'phasedvcfdir'])):
os.makedirs(phase_path)
initialize0(phase_path, cancer_dir_path)
for cnv_path in cnv_list:
initialize_pipeline(phase_path, haplotype_path, cnv_path)
pool1 = multiprocessing.Pool(
processes=12,
initializer=initPool,
initargs=[logQueue, logger.getEffectiveLevel(), terminating])
try:
if not params.GetSplitBamsPath():
if not os.path.exists("/".join([res_path, 'splitbams'])):
os.makedirs("/".join([res_path, 'splitbams']))
params.SetSplitBamsPath("/".join([res_path, 'splitbams']))
result0 = pool1.map_async(split_bam_by_chr,
chromosome_event).get(9999999)
result1 = pool1.map_async(find_roi_bam, chromosome_event).get(9999999)
result2 = pool1.map_async(implement_cnv, chromosome_event).get(9999999)
pool1.close()
except KeyboardInterrupt:
logger.debug('You cancelled the program!')
pool1.terminate()
except Exception as e:
logger.exception("Exception in main %s", e)
pool1.terminate()
finally:
pool1.join()
time.sleep(.1)
mergeSortBamFiles(outbamfn, finalbams_path)
t1 = time.time()
shutil.rmtree(tmpbams_path)
logger.debug(' ***** pipeline finished in ' +
str(round((t1 - t0) / 60.0, 1)) + ' minutes ***** ')
logging.shutdown()
