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_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)