def test_simple(self):
specification = "-l h_vmem=16G -pe smp 8"
with drmaa.Session() as session:
jobManager = JobManagerDRMAA(getPath("tests/output/manager"), getPath("tests/output/manager/log"), session, None)
self.assertEquals(jobManager.extractSpecification, None)
jobManager.setExtractSpecification(specification)
self.assertEquals(jobManager.extractSpecification, specification)
def test_simple(self):
specification = "-l h_vmem=16G -pe smp 8"
with drmaa.Session() as session:
jobManager = JobManagerDRMAA(getPath("tests/output/manager"),
getPath("tests/output/manager/log"),
session, None)
self.assertEquals(jobManager.extractSpecification, None)
jobManager.setExtractSpecification(specification)
self.assertEquals(jobManager.extractSpecification, specification)
def test_simple(self):
with drmaa.Session() as session:
outputDirectoryLocation = getPath("tests/output/manager")
logDirectoryLocation = getPath("tests/output/manager/log")
specification = "-l h_vmem=2G -pe smp 1"
jobManager = JobManagerDRMAA(outputDirectoryLocation, logDirectoryLocation, session, None)
jobManager.setExtractSpecification(specification)
referenceLocation = "tests/data/manager/simple.fasta"
referenceSize = 12
rate = 0.01
inclusion = ["tests/data/manager/simple.fasta", "tests/data/manager/alternative.fasta"]
inhits = 2
exclusion = ["tests/data/manager/simple.fasta", "tests/data/manager/alternative.fasta"]
exhits = 2
gap = 3
size = 5
GC = 0.5
confidence = 0.95
aggregateLocation = "tests/data/manager/simple.kmers"
outputLocation = getPath("tests/output/manager/temp.out")
job = jobManager.createExtractJob(referenceLocation, referenceSize, rate, inclusion, inhits,
exclusion, exhits, gap, size, GC, confidence, aggregateLocation, outputLocation)
args = [
ExtractSignatures.REFERENCE_LONG, str(referenceLocation),
ExtractSignatures.REFERENCE_SIZE_LONG, str(referenceSize),
ExtractSignatures.RATE_LONG, str(rate),
ExtractSignatures.INCLUSION_LONG, "tests/data/manager/simple.fasta", "tests/data/manager/alternative.fasta",
ExtractSignatures.INHITS_LONG, str(inhits),
ExtractSignatures.EXCLUSION_LONG, "tests/data/manager/simple.fasta", "tests/data/manager/alternative.fasta",
ExtractSignatures.EXHITS_LONG, str(exhits),
ExtractSignatures.GAP_LONG, str(gap),
ExtractSignatures.SIZE_LONG, str(size),
ExtractSignatures.GC_LONG, str(GC),
ExtractSignatures.CONFIDENCE_LONG, str(confidence),
ExtractSignatures.KMERS_LONG, aggregateLocation,
ExtractSignatures.OUTPUT_LONG, outputLocation]
self.assertEquals(job.outputPath, ":" + os.path.join(logDirectoryLocation, "Neptune-ExtractSignatures1.o"))
self.assertEquals(job.errorPath, ":" + os.path.join(logDirectoryLocation, "Neptune-ExtractSignatures1.e"))
self.assertEquals(job.args[1:], args)
self.assertEquals(job.nativeSpecification, specification)
def test_simple(self):
with drmaa.Session() as session:
outputDirectoryLocation = getPath("tests/output/manager")
logDirectoryLocation = getPath("tests/output/manager/log")
specification = "-l h_vmem=2G -pe smp 1"
jobManager = JobManagerDRMAA(outputDirectoryLocation,
logDirectoryLocation, session, None)
jobManager.setExtractSpecification(specification)
referenceLocation = "tests/data/manager/simple.fasta"
referenceSize = 12
rate = 0.01
inclusion = [
"tests/data/manager/simple.fasta",
"tests/data/manager/alternative.fasta"
]
inhits = 2
exclusion = [
"tests/data/manager/simple.fasta",
"tests/data/manager/alternative.fasta"
]
exhits = 2
gap = 3
size = 5
GC = 0.5
confidence = 0.95
aggregateLocation = "tests/data/manager/simple.kmers"
outputLocation = getPath("tests/output/manager/temp.out")
job = jobManager.createExtractJob(referenceLocation, referenceSize,
rate, inclusion, inhits,
exclusion, exhits, gap, size, GC,
confidence, aggregateLocation,
outputLocation)
args = [
ExtractSignatures.REFERENCE_LONG,
str(referenceLocation), ExtractSignatures.REFERENCE_SIZE_LONG,
str(referenceSize), ExtractSignatures.RATE_LONG,
str(rate), ExtractSignatures.INCLUSION_LONG,
"tests/data/manager/simple.fasta",
"tests/data/manager/alternative.fasta",
ExtractSignatures.INHITS_LONG,
str(inhits), ExtractSignatures.EXCLUSION_LONG,
"tests/data/manager/simple.fasta",
"tests/data/manager/alternative.fasta",
ExtractSignatures.EXHITS_LONG,
str(exhits), ExtractSignatures.GAP_LONG,
str(gap), ExtractSignatures.SIZE_LONG,
str(size), ExtractSignatures.GC_LONG,
str(GC), ExtractSignatures.CONFIDENCE_LONG,
str(confidence), ExtractSignatures.KMERS_LONG,
aggregateLocation, ExtractSignatures.OUTPUT_LONG,
outputLocation
]
self.assertEquals(
job.outputPath, ":" + os.path.join(
logDirectoryLocation, "Neptune-ExtractSignatures1.o"))
self.assertEquals(
job.errorPath, ":" + os.path.join(
logDirectoryLocation, "Neptune-ExtractSignatures1.e"))
self.assertEquals(job.args[1:], args)
self.assertEquals(job.nativeSpecification, specification)
