def run(self):
cmd = self.args.subCommand
try:
if cmd == 'merge':
cmpH5Merge(self.args.inCmps, self.args.outCmp, self.args.referencesFile)
elif cmd == 'sort':
cmpH5Sort(self.args.inCmp, self.args.outCmp, self.args.tmpdir,
deep = self.args.deepsort,
useNative = not self.args.usePythonIndexer,
inPlace = self.args.inPlace)
elif cmd == 'select':
cmpH5Select(self.args.inCmp, self.args.outCmp,
idxs = self.args.idxs, whereStr = self.args.where,
groupByStr = self.args.groupBy,
groupByCsv = self.args.groupByCsv,
outDir = self.args.outDir)
elif cmd == 'stats':
cmpH5Stats(self.args.inCmp,
whatStr = self.args.what,
whereStr = self.args.where,
groupByStr = self.args.groupBy,
sortByStr = self.args.sortBy,
limit = self.args.limit,
outFile = self.args.outCsv)
elif cmd == 'listMetrics':
print '--- Metrics:'
print "\t\n".join(DocumentedMetric.list())
print '\n--- Statistics:'
print "\t\n".join(DocumentedStatistic.list())
elif cmd == 'equal':
ret = cmpH5Equal(self.args.inCmp1, self.args.inCmp2)
if not ret[0]:
print >> sys.stderr, ret[1]
return 1
else:
return 0
elif cmd == 'summarize':
for inCmp in self.args.inCmps:
print "".join(["-"] * 40)
print cmpH5Summarize(inCmp)
elif cmd == 'validate':
if cmpH5Validate(self.args.inCmp):
return 0
else:
return 1
else:
raise PBH5ToolsException("", "Unkown command passed to cmph5tools.py:" +
self.args.subName)
return 0
except PBH5ToolsException as pbe:
logging.exception(pbe)
return 1
def test_basic(self):
b1 = 'F_42--R_42'
b2 = 'F_28--R_28'
where = "(Barcode == '{b1}') | (Barcode == '{b2}')".format(b1=b1,
b2=b2)
outFile = self._getTempFile(suffix="_.cmp.h5")
# this interface doesn't really make sense. The outFile is required,
# but it is never used.
cmpH5Select(_CMP_H5,
outFile,
groupByStr="Barcode",
whereStr=where,
outDir=self.dirName)
#n = _getNAlignments(outFile)
#self.assertEqual(n, 85)
nalignmentsTuple = [(b1, 76), (b2, 9)]
for b, nalignments in nalignmentsTuple:
p = os.path.join(self.dirName, b + ".cmp.h5")
self.assertTrue(os.path.exists(p),
"Unable to find {b}".format(b=p))
n = _getNAlignments(p)
_d = dict(n=n, m=nalignments, p=p)
msg = "Incorrect alignments (got {n} expected {m} ) from {p}".format(
**_d)
self.assertEqual(n, nalignments, msg)
def test_basic(self):
b1 = 'F_42--R_42'
b2 = 'F_28--R_28'
where = "(Barcode == '{b1}') | (Barcode == '{b2}')".format(b1=b1, b2=b2)
outFile = self._getTempFile(suffix="_.cmp.h5")
# this interface doesn't really make sense. The outFile is required,
# but it is never used.
cmpH5Select(_CMP_H5, outFile, groupByStr="Barcode",
whereStr=where, outDir=self.dirName)
#n = _getNAlignments(outFile)
#self.assertEqual(n, 85)
nalignmentsTuple = [(b1, 76), (b2, 9)]
for b, nalignments in nalignmentsTuple:
p = os.path.join(self.dirName, b + ".cmp.h5")
self.assertTrue(os.path.exists(p), "Unable to find {b}".format(b=p))
n = _getNAlignments(p)
_d = dict(n=n, m=nalignments, p=p)
msg = "Incorrect alignments (got {n} expected {m} ) from {p}".format(**_d)
self.assertEqual(n, nalignments, msg)
def run(self):
cmd = self.args.subCommand
try:
if cmd == 'merge':
cmpH5Merge(self.args.inCmps, self.args.outCmp,
self.args.referencesFile)
elif cmd == 'sort':
cmpH5Sort(self.args.inCmp,
self.args.outCmp,
self.args.tmpdir,
deep=self.args.deepsort,
useNative=not self.args.usePythonIndexer,
inPlace=self.args.inPlace)
elif cmd == 'select':
cmpH5Select(self.args.inCmp,
self.args.outCmp,
idxs=self.args.idxs,
whereStr=self.args.where,
groupByStr=self.args.groupBy,
groupByCsv=self.args.groupByCsv,
outDir=self.args.outDir)
elif cmd == 'stats':
cmpH5Stats(self.args.inCmp,
whatStr=self.args.what,
whereStr=self.args.where,
groupByStr=self.args.groupBy,
sortByStr=self.args.sortBy,
limit=self.args.limit,
outFile=self.args.outCsv)
elif cmd == 'listMetrics':
print '--- Metrics:'
print "\t\n".join(DocumentedMetric.list())
print '\n--- Statistics:'
print "\t\n".join(DocumentedStatistic.list())
elif cmd == 'equal':
ret = cmpH5Equal(self.args.inCmp1, self.args.inCmp2)
if not ret[0]:
print >> sys.stderr, ret[1]
return 1
else:
return 0
elif cmd == 'summarize':
for inCmp in self.args.inCmps:
print "".join(["-"] * 40)
print cmpH5Summarize(inCmp)
elif cmd == 'validate':
if cmpH5Validate(self.args.inCmp):
return 0
else:
return 1
else:
raise PBH5ToolsException(
"", "Unkown command passed to cmph5tools.py:" +
self.args.subName)
return 0
except PBH5ToolsException as pbe:
logging.exception(pbe)
return 1