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.setDatabaseSpecification(specification)
inputLocations = ["tests/data/manager/simple.fasta", "tests/data/manager/alternative.fasta"]
aggregatedLocation = getPath("tests/output/manager/aggregated.out")
outputLocation = getPath("tests/output/manager/temp.out")
job = jobManager.createDatabaseJob(inputLocations, aggregatedLocation, outputLocation)
args = [
"-dbtype", "nucl",
"-in", aggregatedLocation,
"-title", "DATABASE",
"-out", outputLocation]
self.assertEquals(job.outputPath, ":" + os.path.join(logDirectoryLocation, "Neptune-CreateDatabase1.o"))
self.assertEquals(job.errorPath, ":" + os.path.join(logDirectoryLocation, "Neptune-CreateDatabase1.e"))
self.assertEquals(job.args, args)
self.assertEquals(job.nativeSpecification, specification)
def test_no_tag(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.setAggregateSpecification(specification)
inclusionLocations = ["tests/data/manager/simple.fasta", "tests/data/manager/alternative.fasta"]
exclusionLocations = ["tests/data/manager/simple.fasta", "tests/data/manager/alternative.fasta"]
outputLocation = getPath("tests/output/manager/temp.out")
tag = None
job = jobManager.createAggregateJob(inclusionLocations, exclusionLocations, outputLocation, tag)
args = [
AggregateKMers.INCLUSION_LONG, "tests/data/manager/simple.fasta", "tests/data/manager/alternative.fasta",
AggregateKMers.EXCLUSION_LONG, "tests/data/manager/simple.fasta", "tests/data/manager/alternative.fasta",
AggregateKMers.OUTPUT_LONG, outputLocation,
AggregateKMers.DELETE_LONG]
self.assertEquals(job.outputPath, ":" + os.path.join(logDirectoryLocation, "Neptune-AggregateKMers1.o"))
self.assertEquals(job.errorPath, ":" + os.path.join(logDirectoryLocation, "Neptune-AggregateKMers1.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")
logDirectoryLocation = getPath("tests/output/log")
specification = "-l h_vmem=2G -pe smp 1"
jobManager = JobManagerDRMAA(outputDirectoryLocation, logDirectoryLocation, session, None)
jobManager.setCountSpecification(specification)
inputLocation = "tests/data/manager/simple.fasta"
outputLocation = getPath("tests/output/manager/temp.out")
k = 7
organization = 0
job = jobManager.createCountJob(inputLocation, outputLocation, k, organization)
args = [
CountKMers.INPUT_LONG, str(inputLocation),
CountKMers.OUTPUT_LONG, str(outputLocation),
CountKMers.KMER_LONG, str(k),
CountKMers.ORGANIZATION_LONG, str(organization)]
self.assertEquals(job.outputPath, ":" + os.path.join(logDirectoryLocation, "Neptune-CountKMers1.o"))
self.assertEquals(job.errorPath, ":" + os.path.join(logDirectoryLocation, "Neptune-CountKMers1.e"))
self.assertEquals(job.args[1:], args)
self.assertEquals(job.nativeSpecification, 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.consolidateSpecification, None)
jobManager.setConsolidateSpecification(specification)
self.assertEquals(jobManager.consolidateSpecification, specification)
def test_simple(self):
with drmaa.Session() as session:
outputDirectoryLocation = getPath("tests/output/manager")
logDirectoryLocation = getPath("tests/output/manager/log")
defaultSpecification = "-l h_vmem=2G -pe smp 1"
jobManager = JobManagerDRMAA(outputDirectoryLocation, logDirectoryLocation, session, defaultSpecification)
job = jobManager.createJob()
self.assertTrue(job)
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.filterSpecification, None)
jobManager.setFilterSpecification(specification)
self.assertEquals(jobManager.filterSpecification, specification)
def test_simple(self):
with drmaa.Session() as session:
outputDirectoryLocation = getPath("tests/output/manager")
logDirectoryLocation = getPath("tests/output/manager/log")
defaultSpecification = "-l h_vmem=2G -pe smp 1"
jobManager = JobManagerDRMAA(outputDirectoryLocation,
logDirectoryLocation, session,
defaultSpecification)
job = jobManager.createJob()
self.assertTrue(job)
def test_defaults(self):
with drmaa.Session() as session:
outputDirectoryLocation = getPath("tests/output/manager")
logDirectoryLocation = getPath("tests/output/manager/log")
defaultSpecification = "-l h_vmem=16G -pe smp 8"
jobManager = JobManagerDRMAA(outputDirectoryLocation,
logDirectoryLocation, session,
defaultSpecification)
self.assertEquals(jobManager.session, session)
self.assertEquals(jobManager.outputDirectoryLocation,
outputDirectoryLocation)
self.assertEquals(jobManager.countSpecification,
defaultSpecification)
self.assertEquals(jobManager.aggregateSpecification,
defaultSpecification)
self.assertEquals(jobManager.extractSpecification,
defaultSpecification)
self.assertEquals(jobManager.databaseSpecification,
defaultSpecification)
self.assertEquals(jobManager.filterSpecification,
defaultSpecification)
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_no_tag(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.setAggregateSpecification(specification)
inclusionLocations = [
"tests/data/manager/simple.fasta",
"tests/data/manager/alternative.fasta"
]
exclusionLocations = [
"tests/data/manager/simple.fasta",
"tests/data/manager/alternative.fasta"
]
outputLocation = getPath("tests/output/manager/temp.out")
tag = None
job = jobManager.createAggregateJob(inclusionLocations,
exclusionLocations,
outputLocation, tag)
args = [
AggregateKMers.INCLUSION_LONG,
"tests/data/manager/simple.fasta",
"tests/data/manager/alternative.fasta",
AggregateKMers.EXCLUSION_LONG,
"tests/data/manager/simple.fasta",
"tests/data/manager/alternative.fasta",
AggregateKMers.OUTPUT_LONG, outputLocation,
AggregateKMers.DELETE_LONG
]
self.assertEquals(
job.outputPath, ":" + os.path.join(
logDirectoryLocation, "Neptune-AggregateKMers1.o"))
self.assertEquals(
job.errorPath, ":" + os.path.join(logDirectoryLocation,
"Neptune-AggregateKMers1.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.setFilterSpecification(specification)
inclusionDatabaseLocation = "tests/data/manager/FAKE_IN_DB.FAKE"
exclusionDatabaseLocation = "tests/data/manager/FAKE_EX_DB.FAKE"
inclusion = ["tests/data/manager/simple.fasta", "tests/data/manager/alternative.fasta"]
exclusion = ["tests/data/manager/simple.fasta", "tests/data/manager/alternative.fasta"]
inputLocation = "tests/data/manager/simple.fasta"
filteredOutputLocation = getPath("tests/output/manager/simple.filtered")
sortedOutputLocation = getPath("tests/output/manager/simple.sorted")
filterLength = 0.5
filterPercent = 0.5
seedSize = 11
job = jobManager.createFilterJob(inclusionDatabaseLocation, exclusionDatabaseLocation,
inclusion, exclusion, inputLocation, filteredOutputLocation, sortedOutputLocation,
filterLength, filterPercent, seedSize)
args = [
FilterSignatures.INCLUSION_DATABASE_LONG, str(inclusionDatabaseLocation),
FilterSignatures.EXCLUSION_DATABASE_LONG, str(exclusionDatabaseLocation),
FilterSignatures.INCLUSION_LONG, "tests/data/manager/simple.fasta", "tests/data/manager/alternative.fasta",
FilterSignatures.EXCLUSION_LONG, "tests/data/manager/simple.fasta", "tests/data/manager/alternative.fasta",
FilterSignatures.INPUT_LONG, str(inputLocation),
FilterSignatures.FILTERED_OUTPUT_LONG, str(filteredOutputLocation),
FilterSignatures.SORTED_OUTPUT_LONG, str(sortedOutputLocation),
FilterSignatures.FILTER_LENGTH_LONG, str(filterLength),
FilterSignatures.FILTER_PERCENT_LONG, str(filterPercent),
FilterSignatures.SEED_SIZE_LONG, str(seedSize)]
self.assertEquals(job.outputPath, ":" + os.path.join(logDirectoryLocation, "Neptune-FilterSignatures1.o"))
self.assertEquals(job.errorPath, ":" + os.path.join(logDirectoryLocation, "Neptune-FilterSignatures1.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.setDatabaseSpecification(specification)
inputLocations = [
"tests/data/manager/simple.fasta",
"tests/data/manager/alternative.fasta"
]
aggregatedLocation = getPath("tests/output/manager/aggregated.out")
outputLocation = getPath("tests/output/manager/temp.out")
job = jobManager.createDatabaseJob(inputLocations,
aggregatedLocation,
outputLocation)
args = [
"-dbtype", "nucl", "-in", aggregatedLocation, "-title",
"DATABASE", "-out", outputLocation
]
self.assertEquals(
job.outputPath, ":" + os.path.join(
logDirectoryLocation, "Neptune-CreateDatabase1.o"))
self.assertEquals(
job.errorPath, ":" + os.path.join(logDirectoryLocation,
"Neptune-CreateDatabase1.e"))
self.assertEquals(job.args, args)
self.assertEquals(job.nativeSpecification, specification)
def test_simple(self):
with drmaa.Session() as session:
outputDirectoryLocation = getPath("tests/output")
logDirectoryLocation = getPath("tests/output/log")
specification = "-l h_vmem=2G -pe smp 1"
jobManager = JobManagerDRMAA(outputDirectoryLocation,
logDirectoryLocation, session, None)
jobManager.setCountSpecification(specification)
inputLocation = "tests/data/manager/simple.fasta"
outputLocation = getPath("tests/output/manager/temp.out")
k = 7
organization = 0
job = jobManager.createCountJob(inputLocation, outputLocation, k,
organization)
args = [
CountKMers.INPUT_LONG,
str(inputLocation), CountKMers.OUTPUT_LONG,
str(outputLocation), CountKMers.KMER_LONG,
str(k), CountKMers.ORGANIZATION_LONG,
str(organization)
]
self.assertEquals(
job.outputPath, ":" +
os.path.join(logDirectoryLocation, "Neptune-CountKMers1.o"))
self.assertEquals(
job.errorPath, ":" +
os.path.join(logDirectoryLocation, "Neptune-CountKMers1.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.setFilterSpecification(specification)
inclusionDatabaseLocation = "tests/data/manager/FAKE_IN_DB.FAKE"
exclusionDatabaseLocation = "tests/data/manager/FAKE_EX_DB.FAKE"
inclusion = [
"tests/data/manager/simple.fasta",
"tests/data/manager/alternative.fasta"
]
exclusion = [
"tests/data/manager/simple.fasta",
"tests/data/manager/alternative.fasta"
]
inputLocation = "tests/data/manager/simple.fasta"
filteredOutputLocation = getPath(
"tests/output/manager/simple.filtered")
sortedOutputLocation = getPath(
"tests/output/manager/simple.sorted")
filterLength = 0.5
filterPercent = 0.5
seedSize = 11
job = jobManager.createFilterJob(
inclusionDatabaseLocation, exclusionDatabaseLocation,
inclusion, exclusion, inputLocation, filteredOutputLocation,
sortedOutputLocation, filterLength, filterPercent, seedSize)
args = [
FilterSignatures.INCLUSION_DATABASE_LONG,
str(inclusionDatabaseLocation),
FilterSignatures.EXCLUSION_DATABASE_LONG,
str(exclusionDatabaseLocation),
FilterSignatures.INCLUSION_LONG,
"tests/data/manager/simple.fasta",
"tests/data/manager/alternative.fasta",
FilterSignatures.EXCLUSION_LONG,
"tests/data/manager/simple.fasta",
"tests/data/manager/alternative.fasta",
FilterSignatures.INPUT_LONG,
str(inputLocation), FilterSignatures.FILTERED_OUTPUT_LONG,
str(filteredOutputLocation),
FilterSignatures.SORTED_OUTPUT_LONG,
str(sortedOutputLocation), FilterSignatures.FILTER_LENGTH_LONG,
str(filterLength), FilterSignatures.FILTER_PERCENT_LONG,
str(filterPercent), FilterSignatures.SEED_SIZE_LONG,
str(seedSize)
]
self.assertEquals(
job.outputPath, ":" + os.path.join(
logDirectoryLocation, "Neptune-FilterSignatures1.o"))
self.assertEquals(
job.errorPath, ":" + os.path.join(
logDirectoryLocation, "Neptune-FilterSignatures1.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)
