def loadStatsXml(args):
dset = DataSet(args.infile, strict=args.strict)
dset.loadStats(args.statsfile)
if args.outfile:
dset.write(args.outfile, validate=False)
else:
dset.write(args.infile, validate=False)
def loadStatsXml(args):
dset = DataSet(args.infile, strict=args.strict)
dset.loadStats(args.statsfile)
if args.outfile:
dset.write(args.outfile, validate=False)
else:
dset.write(args.infile, validate=False)
def test_build(self):
# Progs like pbalign provide a .bam file:
# e.g. d = DataSet("aligned.bam")
# Something like the test files we have:
inBam = data.getBam()
self.assertTrue(inBam.endswith('.bam'))
d = DataSet(inBam)
# A UniqueId is generated, despite being a BAM input
self.assertTrue(d.uuid != '')
dOldUuid = d.uuid
# They can write this BAM to an XML:
# e.g. d.write("alignmentset.xml")
outdir = tempfile.mkdtemp(suffix="dataset-unittest")
outXml = os.path.join(outdir, 'tempfile.xml')
d.write(outXml)
# And then recover the same XML (or a different one):
# e.g. d = DataSet("alignmentset.xml")
d = DataSet(outXml)
# The UniqueId will be the same
self.assertTrue(d.uuid == dOldUuid)
# Inputs can be many and varied
ds1 = DataSet(data.getXml(11), data.getBam())
self.assertEquals(ds1.numExternalResources, 2)
ds1 = DataSet(data.getFofn())
self.assertEquals(ds1.numExternalResources, 2)
# New! Use the correct constructor:
self.assertEquals(type(SubreadSet(data.getSubreadSet())).__name__,
'SubreadSet')
# Even with untyped inputs
self.assertTrue(str(SubreadSet(data.getBam())).startswith(
'<SubreadSet'))
self.assertEquals(type(SubreadSet(data.getBam())).__name__,
'SubreadSet')
self.assertEquals(type(DataSet(data.getBam())).__name__,
'DataSet')
# You can also cast up and down, but casting between siblings
# is limited (abuse at your own risk)
self.assertEquals(
type(DataSet(data.getBam()).copy(asType='SubreadSet')).__name__,
'SubreadSet')
self.assertEquals(
type(SubreadSet(data.getBam()).copy(asType='DataSet')).__name__,
'DataSet')
# Add external Resources:
ds = DataSet()
ds.externalResources.addResources(["IdontExist.bam"])
self.assertTrue(
ds.externalResources[-1].resourceId == "IdontExist.bam")
# Add an index file
ds.externalResources[-1].addIndices(["IdontExist.bam.pbi"])
self.assertTrue(
ds.externalResources[-1].indices[0].resourceId ==
"IdontExist.bam.pbi")
def test_build(self):
# Progs like pbalign provide a .bam file:
# e.g. d = DataSet("aligned.bam")
# Something like the test files we have:
inBam = data.getBam()
self.assertTrue(inBam.endswith('.bam'))
d = DataSet(inBam)
# A UniqueId is generated, despite being a BAM input
self.assertTrue(d.uuid != '')
dOldUuid = d.uuid
# They can write this BAM to an XML:
# e.g. d.write("alignmentset.xml")
outdir = tempfile.mkdtemp(suffix="dataset-unittest")
outXml = os.path.join(outdir, 'tempfile.xml')
d.write(outXml)
# And then recover the same XML (or a different one):
# e.g. d = DataSet("alignmentset.xml")
d = DataSet(outXml)
# The UniqueId will be the same
self.assertTrue(d.uuid == dOldUuid)
# Inputs can be many and varied
ds1 = DataSet(data.getXml(11), data.getBam())
self.assertEquals(ds1.numExternalResources, 2)
ds1 = DataSet(data.getFofn())
self.assertEquals(ds1.numExternalResources, 2)
# New! Use the correct constructor:
self.assertEquals(
type(SubreadSet(data.getSubreadSet())).__name__, 'SubreadSet')
# Even with untyped inputs
self.assertTrue(
str(SubreadSet(data.getBam())).startswith('<SubreadSet'))
self.assertEquals(
type(SubreadSet(data.getBam())).__name__, 'SubreadSet')
self.assertEquals(type(DataSet(data.getBam())).__name__, 'DataSet')
# You can also cast up and down, but casting between siblings
# is limited (abuse at your own risk)
self.assertEquals(
type(DataSet(data.getBam()).copy(asType='SubreadSet')).__name__,
'SubreadSet')
self.assertEquals(
type(SubreadSet(data.getBam()).copy(asType='DataSet')).__name__,
'DataSet')
# Add external Resources:
ds = DataSet()
ds.externalResources.addResources(["IdontExist.bam"])
self.assertTrue(
ds.externalResources[-1].resourceId == "IdontExist.bam")
# Add an index file
ds.externalResources[-1].addIndices(["IdontExist.bam.pbi"])
self.assertTrue(ds.externalResources[-1].indices[0].resourceId ==
"IdontExist.bam.pbi")
def filterXml(args):
log.error("Adding filters via CLI is temporarily out of order")
exit(1)
if args.infile.endswith('xml'):
dataSet = DataSet(args.infile, strict=args.strict)
filters = []
separators = ['<=', '>=', '!=', '==', '>', '<', '=']
for filt in args.filters:
for sep in separators:
if sep in filt:
param, condition = filt.split(sep)
condition = sep + condition
filters[param] = condition
break
dataSet.addFilters([filters])
log.info("{i} filters added".format(i=len(filters)))
dataSet.write(args.outfile)
else:
raise IOError("No files found/found to be compatible")
def filterXml(args):
log.error("Adding filters via CLI is temporarily out of order")
exit(1)
if args.infile.endswith('xml'):
dataSet = DataSet(args.infile, strict=args.strict)
filters = []
separators = ['<=', '>=', '!=', '==', '>', '<', '=']
for filt in args.filters:
for sep in separators:
if sep in filt:
param, condition = filt.split(sep)
condition = sep + condition
filters[param] = condition
break
dataSet.addFilters([filters])
log.info("{i} filters added".format(i=len(filters)))
dataSet.write(args.outfile)
else:
raise IOError("No files found/found to be compatible")
