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resolve conflict
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@fidelram
fidelram committed May 17, 2017
2 parents dad8e36 + bfa99d5 commit 7b6b186
Showing 1 changed file with 33 additions and 34 deletions.
67 changes: 33 additions & 34 deletions hicexplorer/hicBuildMatrix.py
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Original file line number Diff line number Diff line change
Expand Up @@ -90,6 +90,17 @@ def parse_arguments(args=None):
type=argparse.FileType('r'),
required=True)

parser.add_argument('--outBam', '-b',
help='Bam file to process. Optional parameter. '
'An bam file containing all valid Hi-C reads can be created '
'using this option. This bam file could be useful to inspect '
'the distribution of valid Hi-C reads pairs or for other '
'downstream analysis, but is not used by any HiCExplorer tool. '
'Computation will be significant longer if this option is set.',
metavar='bam file',
type=argparse.FileType('w'),
required=False)

group = parser.add_mutually_exclusive_group(required=True)

group.add_argument('--binSize', '-bs',
Expand Down Expand Up @@ -203,18 +214,6 @@ def parse_arguments(args=None):
default=100000,
type=int
)

parser.add_argument('--outBam', '-b',
help='Bam file to process. Optional parameter. '
'An bam file containing all valid Hi-C reads can be created '
'using this option. This bam file could be useful to inspect '
'the distribution of valid Hi-C reads pairs or for other '
'downstream analysis, but is not used by any HiCExplorer tool. '
'Computation will be significant longer if this option is set.',
metavar='bam file',
type=argparse.FileType('w'),
required=False)

parser.add_argument('--outputFileBufferDir',
help='The location of the output file buffer. At this location the intermediate \'bam\' files and \'bam_done\' are stored. Per default /dev/shm/ is used which is in the most Linux systems a RAM disk. '
'Please make sure no other instance of hicBuildMatrix is accessing this directory at the same time or that old tmp files, maybe from '
Expand Down Expand Up @@ -949,29 +948,30 @@ def process_data(pMateBuffer1, pMateBuffer2, pMinMappingQuality,
return


def write_bam(pOutputBam, pTemplate, pOutputFileBufferDir):
def write_bam(pTemplate, pOutputFileBufferDir, pUniqueHashForBam):

out_bam = pysam.Samfile(os.path.join(pOutputFileBufferDir, pOutputBam), 'wb', template=pTemplate)
out_bam = pysam.Samfile(os.path.join(pOutputFileBufferDir, pUniqueHashForBam + ".bam"), 'wb', template=pTemplate)

counter = 0
while not os.path.isfile(os.path.join(pOutputFileBufferDir, 'done_processing')) or os.path.isfile(os.path.join(pOutputFileBufferDir, str(counter) + '.bam_done')):
if os.path.isfile(os.path.join(pOutputFileBufferDir, str(counter) + '.bam_done')):
out_put_threads = pysam.Samfile(os.path.join(pOutputFileBufferDir, str(counter) + '.bam'), 'rb')
while not os.path.isfile(os.path.join(pOutputFileBufferDir, pUniqueHashForBam + '.done_processing')) \
or os.path.isfile(os.path.join(pOutputFileBufferDir, str(counter) + "_" + pUniqueHashForBam + '.bam_done')):
if os.path.isfile(os.path.join(pOutputFileBufferDir, str(counter) + "_" + pUniqueHashForBam + '.bam_done')):
out_put_threads = pysam.Samfile(os.path.join(pOutputFileBufferDir, str(counter) + "_" + pUniqueHashForBam + '.bam'), 'rb')
while True:
try:
data = out_put_threads.next()
except StopIteration:
break
out_bam.write(data)
out_put_threads.close()
os.remove(os.path.join(pOutputFileBufferDir, str(counter) + '.bam'))
os.remove(os.path.join(pOutputFileBufferDir, str(counter) + '.bam_done'))
os.remove(os.path.join(pOutputFileBufferDir, str(counter) + "_" + pUniqueHashForBam + '.bam'))
os.remove(os.path.join(pOutputFileBufferDir, str(counter) + "_" + pUniqueHashForBam + '.bam_done'))
counter += 1
else:
time.sleep(3)

out_bam.close()
os.remove(os.path.join(pOutputFileBufferDir, 'done_processing'))
os.remove(os.path.join(pOutputFileBufferDir, pUniqueHashForBam + '.done_processing'))


def main(args=None):
Expand Down Expand Up @@ -1007,6 +1007,7 @@ def main(args=None):
args.samFiles[1].close()
outputFileBufferDir = args.outputFileBufferDir
outputFileBufferDir = os.path.join(outputFileBufferDir)
unique_hash_for_bam = str(hash(time.time()))
if args.outBam:
args.outBam.close()

Expand Down Expand Up @@ -1125,8 +1126,8 @@ def main(args=None):
count_output = 0
count_call_of_read_input = 0
computed_pairs = 0
if args.outBam is not None:
process_write_bam_file = Process(target=write_bam, kwargs=dict(pOutputBam=args.outBam.name, pTemplate=str1, pOutputFileBufferDir=outputFileBufferDir))
if args.outBam:
process_write_bam_file = Process(target=write_bam, kwargs=dict(pTemplate=str1, pOutputFileBufferDir=outputFileBufferDir, pUniqueHashForBam=unique_hash_for_bam))
process_write_bam_file.start()
while not all_data_processed or not all_threads_done:

Expand Down Expand Up @@ -1169,7 +1170,7 @@ def main(args=None):
pQueueOut=queue[i],
pTemplate=str1,
pOutputBamSet=args.outBam,
pOutputName=str(count_output) + '.bam',
pOutputName=str(count_output) + "_" + unique_hash_for_bam + '.bam',
pCounter=count_output,
pSharedBinIntvalTree=shared_build_intval_tree,
pDictBinIntervalTreeIndex=index_dict,
Expand Down Expand Up @@ -1217,8 +1218,8 @@ def main(args=None):
process[i].terminate()
process[i] = None
thread_done[i] = True

open(os.path.join(outputFileBufferDir, str(result[0][-1]) + '.bam_done'), 'a').close()
if args.outBam:
open(os.path.join(outputFileBufferDir, str(result[0][-1]) + "_" + unique_hash_for_bam + '.bam_done'), 'a').close()

# caused by the architecture I try to display this output information after +-1e5 of 1e6 reads.
if iter_num % 1e6 < 100000:
Expand Down Expand Up @@ -1251,11 +1252,11 @@ def main(args=None):
# the definite matrix I add the values from the upper and lower triangles
# and subtract the diagonal to avoid double counting it.
# The resulting matrix is symmetric.
open(os.path.join(outputFileBufferDir, 'done_processing'), 'a').close()
print "wait for bam merging process to finish"
if args.outBam is not None:
if args.outBam:
open(os.path.join(outputFileBufferDir, unique_hash_for_bam + '.done_processing'), 'a').close()
print "wait for bam merging process to finish"
process_write_bam_file.join()
print "wait for bam merging process to finish...DONE!"
print "wait for bam merging process to finish...DONE!"

dia = dia_matrix(([hic_matrix.diagonal()], [0]), shape=hic_matrix.shape)
hic_matrix = hic_matrix + hic_matrix.T - dia
Expand All @@ -1282,15 +1283,13 @@ def main(args=None):
args.outFileName.close()
# removing the empty file. Otherwise the save method
# will say that the file already exists.
try:
unlink(args.outFileName.name)
except OSError:
pass
unlink(args.outFileName.name)

hic_ma.save(args.outFileName.name)

if args.outBam:
shutil.move(outputFileBufferDir + args.outBam.name, args.outBam.name)
# os.path.join(outputFileBufferDir, unique_hash_for_bam + "_" + args.outBam.name)
shutil.move(os.path.join(outputFileBufferDir, unique_hash_for_bam + ".bam"), args.outBam.name)

"""
if args.restrictionCutFile:
Expand Down

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