def run_rtc(rtc):
files = list(readFofn(rtc.task.input_files[0]))
report = fofn_to_report(len(files))
shutil.copy(rtc.task.input_files[0], rtc.task.output_files[0])
write_report_and_log(report, rtc.task.output_files[1])
log.info("Completed running {i}".format(i=rtc.task))
return 0
def test_read_ccs_from_multiple_smrtcells_write_one_bam(self):
"""
test_read_ccs_from_multiple_smrtcells_write_one_bam:
Read ccs reads from multiple bam files of multiple SMRTCells,
select records of a few zmws from each movie, and
write to an output bam file.
"""
fofn = op.join(self.bigDataDir, "ccsbam.fofn")
movies = [
"m140802_021814_42161_c110036822550000001823106706241500_s1_p0",
"m140802_043938_42161_c110036822550000001823106706241501_s1_p0",
"m140802_070303_42161_c110036822550000001823106706241502_s1_p0"
]
ccsbamfns = [f for f in readFofn(fofn)]
outbamfn = op.join(self.outDir, "test_writebam_ccs_3.bam")
m1, m2, m3 = movies
hn1 = [54434, 54440, 54493, 80328, 163395]
hn2 = [1784, 7201, 40789, 79704, 152904]
hn3 = [705, 4838, 40197, 84197, 126136]
zmws = ["%s/%d" % (m1, hn) for hn in hn1] + \
["%s/%d" % (m2, hn) for hn in hn2] + \
["%s/%d" % (m3, hn) for hn in hn3]
expected_num_ccs_reads = 13821 + 13457 + 17016 + 13705 + 13581 + 14900 + 13477 + 12238 + 11318 #123513
_verify_write_compare_ccs(self,
ccsbamfns,
zmws,
outbamfn,
expected_movies=movies,
expected_len=expected_num_ccs_reads)
def test_read_ccs_from_multiple_smrtcells_write_one_bam(self):
"""
test_read_ccs_from_multiple_smrtcells_write_one_bam:
Read ccs reads from multiple bam files of multiple SMRTCells,
select records of a few zmws from each movie, and
write to an output bam file.
"""
fofn = op.join(self.bigDataDir, "ccsbam.fofn")
movies = ["m140802_021814_42161_c110036822550000001823106706241500_s1_p0",
"m140802_043938_42161_c110036822550000001823106706241501_s1_p0",
"m140802_070303_42161_c110036822550000001823106706241502_s1_p0"]
ccsbamfns = [f for f in readFofn(fofn)]
outbamfn = op.join(self.outDir, "test_writebam_ccs_3.bam")
m1, m2, m3 = movies
hn1 = [54434, 54440, 54493, 80328, 163395]
hn2 = [1784, 7201, 40789, 79704, 152904]
hn3 = [705, 4838, 40197, 84197, 126136]
zmws = ["%s/%d" % (m1, hn) for hn in hn1] + \
["%s/%d" % (m2, hn) for hn in hn2] + \
["%s/%d" % (m3, hn) for hn in hn3]
expected_num_ccs_reads = 13821 + 13457 + 17016 + 13705 + 13581 + 14900 + 13477 + 12238 + 11318 #123513
_verify_write_compare_ccs(self, ccsbamfns, zmws, outbamfn,
expected_movies=movies,
expected_len=expected_num_ccs_reads)
def fromSmrtPortalPath(jobPath):
# reckon the reports path from the input fofn ...
reportsPaths = set([ updir(path) for path in readFofn(op.join(jobPath, "input.fofn"))])
if len(reportsPaths) > 1:
raise ValueError, "No support for multi-movie jobs yet"
else:
reportsPath = list(reportsPaths)[0]
basFname = findOneOrNone("*.bas.h5", reportsPath) or findOneOrNone("*.bax.h5", reportsPath)
plsFname = findOneOrNone("*.pls.h5", reportsPath) or findOneOrNone("*.plx.h5", reportsPath)
trcFname = findOneOrNone("*.trc.h5", updir(reportsPath))
alnFname = findOneOrNone("*.cmp.h5", op.join(jobPath, "data"))
return Fixture(trcFname=trcFname, plsFname=plsFname,
basFname=basFname, alnFname=alnFname)
def parse_input_file(i_file):
"""Parse input file, get input bam or bax.h5 file."""
bam_fn, bax_fn = None, None
if (i_file.endswith(".bam")):
bam_fn = i_file
elif (i_file.endswith(".fofn")):
fns = [f for f in readFofn(i_file)]
if not all([f.endswith(".bax.h5") for f in fns]) or \
len(fns) != 1:
raise ValueError ("%s fofn should contain exactly one bax.h5 file.")
else:
bax_fn = fns[0]
elif i_file.endswith(".bax.h5"):
bax_fn = i_file
else:
raise ValueError ("Unsupported file format %s" % i_file)
return bam_fn, bax_fn
def parse_input_file(i_file):
"""Parse input file, get input bam or bax.h5 file."""
bam_fn, bax_fn = None, None
if (i_file.endswith(".bam")):
bam_fn = i_file
elif (i_file.endswith(".fofn")):
fns = [f for f in readFofn(i_file)]
if not all([f.endswith(".bax.h5") for f in fns]) or \
len(fns) != 1:
raise ValueError("%s fofn should contain exactly one bax.h5 file.")
else:
bax_fn = fns[0]
elif i_file.endswith(".bax.h5"):
bax_fn = i_file
else:
raise ValueError("Unsupported file format %s" % i_file)
return bam_fn, bax_fn
def fromSmrtPortalPath(jobPath):
# reckon the reports path from the input fofn ...
reportsPaths = set(
[updir(path) for path in readFofn(op.join(jobPath, "input.fofn"))])
if len(reportsPaths) > 1:
raise ValueError, "No support for multi-movie jobs yet"
else:
reportsPath = list(reportsPaths)[0]
basFname = findOneOrNone("*.bas.h5", reportsPath) or findOneOrNone(
"*.bax.h5", reportsPath)
plsFname = findOneOrNone("*.pls.h5", reportsPath) or findOneOrNone(
"*.plx.h5", reportsPath)
trcFname = findOneOrNone("*.trc.h5", updir(reportsPath))
alnFname = findOneOrNone("*.cmp.h5", op.join(jobPath, "data"))
return Fixture(trcFname=trcFname,
plsFname=plsFname,
basFname=basFname,
alnFname=alnFname)
def __init__(self, fname, *rest):
# Can read any of the following:
# ~ fofn
# ~ h5, multipart
# ~ h5, single part
self.filename = op.abspath(op.expanduser(fname))
if fname.endswith(".h5"):
directory = op.dirname(self.filename)
with h5py.File(self.filename, "r") as f:
if f.get("MultiPart"):
partFilenames = [ op.join(directory, fn)
for fn in f["/MultiPart/Parts"] ]
else:
partFilenames = [ self.filename ]
elif self.filename.endswith(".fofn"):
partFilenames = list(readFofn(self.filename))
else:
raise ValueError, "Invalid file name for multipart reader"
self._parts = [ self.PART_READER_CLASS(pfn, *rest)
for pfn in partFilenames ]
def test_simple():
fofn = StringIO("/a/b\n/c/d")
lst = list(readFofn(fofn))
assert_array_equal(["/a/b", "/c/d"], lst)
def test_absolutifying():
for fofnPath in data.getFofns():
for filePath in readFofn(fofnPath):
assert_true(isabs(filePath))
def test_empty_lines():
fofn = StringIO("/a/b\n \n/c/d\n ")
lst = list(readFofn(fofn))
assert_array_equal(["/a/b", "/c/d"], lst)
def test_simple():
fofn = StringIO("/a/b\n/c/d")
lst = list(readFofn(fofn))
assert_array_equal(["/a/b", "/c/d"], lst)
def test_absolutifying():
for fofnPath in data.getFofns():
for filePath in readFofn(fofnPath):
assert_true(isabs(filePath))
def test_simple():
fofn = StringIO("/a/b\n/c/d")
lst = list(readFofn(fofn))
assert ["/a/b", "/c/d"] == lst
def test_empty_lines():
fofn = StringIO(u"/a/b\n \n/c/d\n ")
lst = list(readFofn(fofn))
assert ["/a/b", "/c/d"] == lst