def test_checkReferencePath(self):
"""Test checkReferencePath()."""
refDir = "/pbi/dept/secondary/siv/references/"
refPath = path.join(refDir, "lambda")
refPath, refFastaOut, refSaOut, isWithinRepository, annotation = \
checkReferencePath(refPath)
self.assertTrue(
filecmp.cmp(refFastaOut, path.join(refPath,
"sequence/lambda.fasta")))
self.assertTrue(
filecmp.cmp(refSaOut, path.join(refPath,
"sequence/lambda.fasta.sa")))
self.assertTrue(isWithinRepository)
refpath, refFastaOut, refSaOut, isWithinRepository, annotation = \
checkReferencePath(refFastaOut)
self.assertTrue(
filecmp.cmp(refFastaOut, path.join(refPath,
"sequence/lambda.fasta")))
self.assertTrue(
filecmp.cmp(refSaOut, path.join(refPath,
"sequence/lambda.fasta.sa")))
self.assertTrue(isWithinRepository)
fastaFN = "{0}/data/ecoli.fasta".format(self.rootDir)
refpath, refFastaOut, refSaOut, isWithinRepository, annotation = \
checkReferencePath(fastaFN)
self.assertTrue(filecmp.cmp(refpath, refFastaOut))
self.assertIsNone(refSaOut)
self.assertFalse(isWithinRepository)
refPathWithAnnotation = path.join(DATA_DIR, "references/H1_6_Scal_6x/")
_refPath, _refFaOut, _refSaOut, _isWithinRepository, annotation = \
checkReferencePath(refPathWithAnnotation)
self.assertEqual(
path.abspath(annotation),
path.abspath(
path.join(refPathWithAnnotation,
"annotations/H1_6_Scal_6x_adapters.gff")))
xmlFN = path.join(self.rootDir, "data/reference_lambda.xml")
refpath, refFastaOut, refSaOut, isWithinRepository, annotation = \
checkReferencePath(xmlFN)
self.assertTrue(
filecmp.cmp(
refFastaOut,
"/pbi/dept/secondary/siv/testdata/pbalign-unittest/data/lambda_ref.fasta"
))
def test_checkReferencePath(self):
"""Test checkReferencePath()."""
refDir = "/pbi/dept/secondary/siv/references/"
refPath = path.join(refDir, "lambda")
refPath, refFastaOut, refSaOut, isWithinRepository, annotation = \
checkReferencePath(refPath)
self.assertTrue(filecmp.cmp(refFastaOut,
path.join(refPath,
"sequence/lambda.fasta")))
self.assertTrue(filecmp.cmp(refSaOut,
path.join(refPath,
"sequence/lambda.fasta.sa")))
self.assertTrue(isWithinRepository)
refpath, refFastaOut, refSaOut, isWithinRepository, annotation = \
checkReferencePath(refFastaOut)
self.assertTrue(filecmp.cmp(refFastaOut,
path.join(refPath,
"sequence/lambda.fasta")))
self.assertTrue(filecmp.cmp(refSaOut,
path.join(refPath,
"sequence/lambda.fasta.sa")))
self.assertTrue(isWithinRepository)
fastaFN = "{0}/data/ecoli.fasta".format(self.rootDir)
refpath, refFastaOut, refSaOut, isWithinRepository, annotation = \
checkReferencePath(fastaFN)
self.assertTrue(filecmp.cmp(refpath, refFastaOut))
self.assertIsNone(refSaOut)
self.assertFalse(isWithinRepository)
refPathWithAnnotation = path.join(DATA_DIR, "references/H1_6_Scal_6x/")
_refPath, _refFaOut, _refSaOut, _isWithinRepository, annotation = \
checkReferencePath(refPathWithAnnotation)
self.assertEqual(path.abspath(annotation),
path.abspath(path.join(refPathWithAnnotation,
"annotations/H1_6_Scal_6x_adapters.gff")))
xmlFN = path.join(self.rootDir, "data/reference_lambda.xml")
refpath, refFastaOut, refSaOut, isWithinRepository, annotation = \
checkReferencePath(xmlFN)
self.assertTrue(filecmp.cmp(refFastaOut,
"/pbi/dept/secondary/siv/testdata/pbalign-unittest/data/lambda_ref.fasta"))
def test_checkReferencePath(self):
"""Test checkReferencePath()."""
refDir = "/mnt/secondary/Smrtanalysis/opt/smrtanalysis/common/" + \
"references"
refPath = path.join(refDir, "lambda")
refPath, refFastaOut, refSaOut, isWithinRepository, annotation = \
checkReferencePath(refPath)
self.assertTrue(filecmp.cmp(refFastaOut,
path.join(refPath,
"sequence/lambda.fasta")))
self.assertTrue(filecmp.cmp(refSaOut,
path.join(refPath,
"sequence/lambda.fasta.sa")))
self.assertTrue(isWithinRepository)
refpath, refFastaOut, refSaOut, isWithinRepository, annotation = \
checkReferencePath(refFastaOut)
self.assertTrue(filecmp.cmp(refFastaOut,
path.join(refPath,
"sequence/lambda.fasta")))
self.assertTrue(filecmp.cmp(refSaOut,
path.join(refPath,
"sequence/lambda.fasta.sa")))
self.assertTrue(isWithinRepository)
fastaFN = "{0}/data/ecoli.fasta".format(self.rootDir)
refpath, refFastaOut, refSaOut, isWithinRepository, annotation = \
checkReferencePath(fastaFN)
self.assertTrue(filecmp.cmp(refpath, refFastaOut))
self.assertIsNone(refSaOut)
self.assertFalse(isWithinRepository)
refPathWithAnnotation = "/mnt/secondary-siv/" + \
"testdata/BlasrTestData/pbalign/data/references/H1_6_Scal_6x/"
_refPath, _refFaOut, _refSaOut, _isWithinRepository, annotation = \
checkReferencePath(refPathWithAnnotation)
self.assertEqual(path.abspath(annotation),
path.abspath(path.join(refPathWithAnnotation,
"annotations/H1_6_Scal_6x_adapters.gff")))
def SetReferencePath(self, referencePath):
"""Validate the user-specified referencePath and get the absolute
and expanded path for referencePath, targetFileName and
sawriterFileName. targetFileName is the target reference FASTA
file to be used by an aligner. sawriterFileName is the reference
sawriter file that can be used by an aligner (e.g. blasr), its
value can be None if absent.
"""
if referencePath is not None and referencePath != "":
(self.referencePath, self.targetFileName,
self.sawriterFileName, self.isWithinRepository,
self.adapterGffFileName) = \
checkReferencePath(referencePath)
def SetReferencePath(self, referencePath):
"""Validate the user-specified referencePath and get the absolute
and expanded path for referencePath, targetFileName and
sawriterFileName. targetFileName is the target reference FASTA
file to be used by an aligner. sawriterFileName is the reference
sawriter file that can be used by an aligner (e.g. blasr), its
value can be None if absent.
"""
if referencePath is not None and referencePath != "":
(self.referencePath, self.targetFileName,
self.sawriterFileName, self.isWithinRepository,
self.adapterGffFileName) = \
checkReferencePath(referencePath)
