def test_build_matrix_cooler():
outfile = NamedTemporaryFile(suffix='.cool', delete=False)
outfile.close()
qc_folder = mkdtemp(prefix="testQC_")
args = "-s {} {} --outFileName {} -bs 5000 -b /tmp/test.bam --QCfolder {} --threads 4".format(
sam_R1, sam_R2, outfile.name, qc_folder).split()
hicBuildMatrix.main(args)
test = hm.hiCMatrix(ROOT + "small_test_matrix_parallel.h5")
new = hm.hiCMatrix(outfile.name)
nt.assert_equal(test.matrix.data, new.matrix.data)
# nt.assert_equal(test.cut_intervals, new.cut_intervals)
nt.assert_equal(len(new.cut_intervals), len(test.cut_intervals))
cut_interval_new_ = []
cut_interval_test_ = []
for x in new.cut_intervals:
cut_interval_new_.append(x[:3])
for x in test.cut_intervals:
cut_interval_test_.append(x[:3])
nt.assert_equal(cut_interval_new_, cut_interval_test_)
# print(set(os.listdir(ROOT + "QC/")))
assert are_files_equal(ROOT + "QC/QC.log", qc_folder + "/QC.log")
assert set(os.listdir(ROOT + "QC/")) == set(os.listdir(qc_folder))
os.unlink(outfile.name)
shutil.rmtree(qc_folder)
def test_build_matrix_rf():
outfile = NamedTemporaryFile(suffix='.h5', delete=False)
outfile.close()
qc_folder = mkdtemp(prefix="testQC_")
args = "-s {} {} -rs {} --outFileName {} --QCfolder {} " \
"--restrictionSequence GATC " \
"--danglingSequence GATC " \
"--minDistance 150 " \
"--maxLibraryInsertSize 1500 --threads 4".format(sam_R1, sam_R2, dpnii_file,
outfile.name,
qc_folder).split()
hicBuildMatrix.main(args)
test = hm.hiCMatrix(ROOT + "small_test_rf_matrix.h5")
new = hm.hiCMatrix(outfile.name)
nt.assert_equal(test.matrix.data, new.matrix.data)
nt.assert_equal(test.cut_intervals, new.cut_intervals)
print(set(os.listdir(ROOT + "QC_rc/")))
assert are_files_equal(ROOT + "QC_rc/QC.log", qc_folder + "/QC.log")
assert set(os.listdir(ROOT + "QC_rc/")) == set(os.listdir(qc_folder))
os.unlink(outfile.name)
shutil.rmtree(qc_folder)
def test_build_matrix_restrictionCutFile_eight(
sam1, sam2, outFile, qcFolder, outBam, binSize, restrictionCutFile,
minDistance, maxDistance, maxLibraryInsertSize, restrictionSequence,
danglingSequence, region, removeSelfLigation, minMappingQuality,
threads, inputBufferSize):
# added skipDuplicationCheck
args = "-s {} {} --restrictionCutFile {} --outFileName {} --QCfolder {} " \
"--restrictionSequence {} " \
"--danglingSequence {} " \
"--minDistance {} " \
"--maxLibraryInsertSize {} --threads {} " \
"--removeSelfLigation {} --keepSelfCircles " \
"--minMappingQuality {} --inputBufferSize {} " \
"--doTestRun --skipDuplicationCheck ".format(bam_R1, bam_R2,
restrictionCutFile, outFile.name,
qcFolder, restrictionSequence,
danglingSequence, minDistance,
maxLibraryInsertSize, threads,
removeSelfLigation,
minMappingQuality,
inputBufferSize).split()
hicBuildMatrix.main(args)
os.unlink(outFile.name)
shutil.rmtree(qcFolder)
def test_build_matrix(capsys):
outfile = NamedTemporaryFile(suffix='.h5', delete=False)
outfile.close()
qc_folder = mkdtemp(prefix="testQC_")
args = "-s {} {} --outFileName {} -bs 5000 -b /tmp/test.bam --QCfolder {} --threads 4".format(
sam_R1, sam_R2, outfile.name, qc_folder).split()
hicBuildMatrix.main(args)
test = hm.hiCMatrix(ROOT + "small_test_matrix_parallel.h5")
new = hm.hiCMatrix(outfile.name)
nt.assert_equal(test.matrix.data, new.matrix.data)
nt.assert_equal(test.cut_intervals, new.cut_intervals)
# print("MATRIX NAME:", outfile.name)
print(set(os.listdir(ROOT + "QC/")))
assert are_files_equal(ROOT + "QC/QC.log", qc_folder + "/QC.log")
assert set(os.listdir(ROOT + "QC/")) == set(os.listdir(qc_folder))
# accept delta of 60 kb, file size is around 4.5 MB
assert abs(
os.path.getsize(ROOT + "small_test_matrix_result.bam") -
os.path.getsize("/tmp/test.bam")) < 64000
os.unlink(outfile.name)
shutil.rmtree(qc_folder)
os.unlink("/tmp/test.bam")
def main(args=None):
args = parse_arguments().parse_args(args)
if not os.path.exists(args.QCfolder):
try:
os.makedirs(args.QCfolder)
except OSError as exc: # Guard against race condition
if exc.errno != errno.EEXIST:
raise
outFile = NamedTemporaryFile(suffix='.h5', delete=False)
args_hicBuildMatrix = "--samFiles {} {} --outFileName {} --QCfolder {} --doTestRun --doTestRunLines {} --threads 1 ".format(
args.samFiles[0], args.samFiles[1], outFile.name, args.QCfolder,
str(args.lines)).split()
args_hicBuildMatrix.append('--binSize')
args_hicBuildMatrix.append(str(10000))
if args.restrictionSequence:
args_hicBuildMatrix.append('--restrictionSequence')
for restrictionSequence in args.restrictionSequence:
args_hicBuildMatrix.append(restrictionSequence)
if args.danglingSequence:
args_hicBuildMatrix.append('--danglingSequence')
for danglingSequence in args.danglingSequence:
args_hicBuildMatrix.append(danglingSequence)
if args.danglingSequence:
args_hicBuildMatrix.append('--restrictionCutFile')
for restrictionCutFile in args.restrictionCutFile:
args_hicBuildMatrix.append(restrictionCutFile.name)
log.debug('args_hicBuildMatrix {}'.format(args_hicBuildMatrix))
hicBuildMatrix.main(args_hicBuildMatrix)
def test_build_matrix_restrictionCutFile_four(
sam1, sam2, outFile, qcFolder, outBam, binSize, restrictionCutFile,
minDistance, maxDistance, maxLibraryInsertSize, restrictionSequence,
danglingSequence, region, removeSelfLigation, minMappingQuality,
threads, inputBufferSize):
# test more params with restrictionCutFile (now without region param)
args = "-s {} {} --restrictionCutFile {} --outFileName {} --QCfolder {} " \
"--restrictionSequence {} " \
"--danglingSequence {} " \
"--minDistance {} " \
"--maxLibraryInsertSize {} --threads {} " \
"--removeSelfLigation {} --keepSelfCircles ".format(bam_R1, bam_R2,
restrictionCutFile,
outFile.name, qcFolder,
restrictionSequence,
danglingSequence,
minDistance,
maxLibraryInsertSize,
threads,
removeSelfLigation).split()
hicBuildMatrix.main(args)
os.unlink(outFile.name)
shutil.rmtree(qcFolder)
def test_build_matrix_restrictionCutFile_one(
sam1, sam2, outFile, qcFolder, outBam, binSize, restrictionCutFile,
minDistance, maxDistance, maxLibraryInsertSize, restrictionSequence,
danglingSequence, region, removeSelfLigation, minMappingQuality,
threads, inputBufferSize):
# test restrictionCutFile
args = "-s {} {} --restrictionCutFile {} --outFileName {} " \
"--QCfolder {} ".format(sam1, sam2,
restrictionCutFile,
outFile.name,
qcFolder).split()
hicBuildMatrix.main(args)
os.unlink(outFile.name)
shutil.rmtree(qcFolder)
def test_build_matrix():
outfile = NamedTemporaryFile(suffix='.h5', delete=False)
outfile.close()
qc_folder = mkdtemp(prefix="testQC_")
args = "-s {} {} -o {} -bs 5000 -b /tmp/test.bam --QCfolder {}".format(
sam_R1, sam_R2, outfile.name, qc_folder).split()
hicBuildMatrix.main(args)
test = hm.hiCMatrix(ROOT + "small_test_matrix.h5")
new = hm.hiCMatrix(outfile.name)
nt.assert_equal(test.matrix.data, new.matrix.data)
assert test.cut_intervals == new.cut_intervals
print set(os.listdir(ROOT + "QC/"))
assert set(os.listdir(ROOT + "QC/")) == set(os.listdir(qc_folder))
os.unlink(outfile.name)
shutil.rmtree(qc_folder)
def test_build_matrix_bin_size(sam1, sam2, outFile, qcFolder, outBam, binSize,
restrictionCutFile, minDistance, maxDistance,
maxLibraryInsertSize, restrictionSequence,
danglingSequence, region, removeSelfLigation,
minMappingQuality, threads, inputBufferSize):
"""
This test runs buildMatrix with all command line args for one time to ensure all args
being ok.
Note: Test will take some time.
Note: parameters can be expanded (the values in the list) so that many combinations of
command line args can be tested.
"""
# test binSize instead of restrictionCutFile
args = "-s {} {} --binSize {} --outFileName {} --QCfolder {} ".format(
sam1, sam2, binSize, outFile.name, qcFolder).split()
hicBuildMatrix.main(args)
os.unlink(outFile.name)
shutil.rmtree(qcFolder)
