def testInitializingDatasources(self):
""" Test initializing a database dir, both single and multicore. This test is RAM intensive and requires default data corpus."""
multiDS = DatasourceFactory.createDatasources(self.config.get(
"DEFAULT", "dbDir"),
"hg19",
isMulticore=True)
self.assertTrue(multiDS is not None, "Datasource list was None")
self.assertTrue(len(multiDS) != 0, "Datasource list was empty")
for i in range(0, len(multiDS)):
self.assertTrue(multiDS[i] is not None,
"multi core datasource was None: " + str(i))
self.assertTrue(isinstance(multiDS[i], Datasource))
# This test can be memory intensive, so get rid of the multiDS, but record how many datasources were created.
numMultiDS = len(multiDS)
del multiDS
singleCoreDS = DatasourceFactory.createDatasources(self.config.get(
"DEFAULT", "dbDir"),
"hg19",
isMulticore=False)
self.assertTrue(singleCoreDS is not None, "Datasource list was None")
self.assertTrue(len(singleCoreDS) != 0, "Datasource list was empty")
for i in range(0, len(singleCoreDS)):
self.assertTrue(singleCoreDS[i] is not None,
"single core datasource was None: " + str(i))
self.assertTrue(isinstance(singleCoreDS[i], Datasource))
self.assertTrue(
numMultiDS == len(singleCoreDS),
"Length of single core datasource list was not the same as multicore"
)
del singleCoreDS
def testBasicDatasourceSorting(self):
"""Test that the GAF datasource is sorted before a gene-based datasource"""
gafDatasource = TestUtils.createTranscriptProviderDatasource(self.config)
geneDS = DatasourceFactory.createDatasource("testdata/small_tsv_ds/small_tsv_ds.config", "testdata/small_tsv_ds/")
incorrectSortList = [geneDS, gafDatasource]
guessSortList = DatasourceFactory.sortDatasources(incorrectSortList)
self.assertTrue(guessSortList[1] == geneDS, "Sorting is incorrect.")
self.assertTrue(len(guessSortList) == 2, "Sorting altered number of datasources (gt: 2): " + str(len(guessSortList)))
def testAnnotateListOfMutations(self):
"""Test that we can initialize an Annotator, without an input or output and then feed mutations,
one at a time... using a runspec"""
# Locate the datasource directory and create a runspec
dbDir = self.config.get("DEFAULT", "dbDir")
ds = DatasourceFactory.createDatasources(dbDir)
runSpec = RunSpecification()
runSpec.initialize(None, None, datasources=ds)
# Initialize the annotator with the runspec
annotator = Annotator()
annotator.initialize(runSpec)
m = MutationData()
m.chr = "1"
m.start = "12941796"
m.end = "12941796"
m.alt_allele = "G"
m.ref_allele = "T"
muts = [m]
muts = annotator.annotate_mutations(muts)
m2 = muts.next()
self.assertTrue(m2.get("gene", None) is not None)
def testESPCoverageAnnotationWithMissingAnnotationValuesIndelAvgMatch(
self):
"""
"""
self.logger.info("Initializing ESP6500SI-V2 Coverage")
tabixIndexedTsvDirName = os.path.join(
*["testdata", "small_esp_coverage_avg_ds", "hg19"])
tabixIndexedTsvDatasource = DatasourceFactory.createDatasource(
os.path.join(tabixIndexedTsvDirName,
"small_esp_coverage_avg_ds.config"),
tabixIndexedTsvDirName)
m1 = MutationData()
m1.chr = "X"
m1.start = "100075350"
m1.end = "100075356"
m1_annotated = tabixIndexedTsvDatasource.annotate_mutation(m1)
m1_annotation = m1_annotated.getAnnotation("ESP_AvgSampleReadDepth")
cur_annotation = Annotation(
value="91.25",
datasourceName="ESP",
dataType="Float",
description="",
tags=[TagConstants.INFO, TagConstants.NOT_SPLIT],
number=None)
self.assertTrue(m1_annotation.isEqual(cur_annotation),
"Annotations do not match.")
def _create_test_ds(self, input_tsv, dir_name, index_cols):
base_name = "test_snp_leveldb"
full_name = dir_name + "/" + base_name
if os.path.exists(full_name):
shutil.rmtree(full_name)
os.makedirs(full_name)
tsv_reader = GenericTsvReader(input_tsv, commentPrepend="%")
annotation_cols = copy.copy(tsv_reader.getFieldNames())
for icol in index_cols:
if icol in annotation_cols:
annotation_cols.remove(icol)
ds_creator = SnpOnlyLevelDbDatasourceCreator()
ds_creator.createDatasource(full_name, input_tsv, ",".join(index_cols), full_name + "/" + base_name + ".config", "snp_leveldb", base_name, "TEST",
"exact", annotation_cols, [])
config_filename = "out/test_simple_annotate_snp_only_leveldb/test_snp_leveldb/test_snp_leveldb.config"
ds = DatasourceFactory.createDatasource(os.path.abspath(config_filename), os.path.dirname(config_filename))
return ds
def testTCGAMAFAsInputAndQuickAnnotate(self):
""" Test that we can take in a TCGA MAF (using MAFLITE), do annotating, and still render it properly """
inputFilename = "testdata/maf/Patient0.maf.annotated"
tmp = MafliteInputMutationCreator(inputFilename, 'configs/maflite_input.config')
outputFilename = "out/testTCGAMAFAsInputAndQuickAnnotate.tsv"
outputRenderer = TcgaMafOutputRenderer(outputFilename, 'configs/tcgaMAF2.4_output.config')
annotator = Annotator()
annotator.setInputCreator(tmp)
annotator.setOutputRenderer(outputRenderer)
ds = DatasourceFactory.createDatasource("testdata/thaga_janakari_gene_ds/hg19/tj_data.config", "testdata/thaga_janakari_gene_ds/hg19/")
annotator.addDatasource(ds)
annotator.annotate()
statinfo = os.stat(outputFilename)
self.assertTrue(statinfo.st_size > 0, "Generated MAF file (" + outputFilename + ") is empty.")
tsvReaderIn = GenericTsvReader(inputFilename)
tsvReader = GenericTsvReader(outputFilename)
self.assertTrue(tsvReader.getComments().find('#version') != -1, "First line did not specify a version number")
self.assertTrue("i_TJ_Data_Why" in tsvReader.getFieldNames(), "New field missing (i_TJ_Data_Why) from header")
self.assertTrue("i_TJ_Data_Who" in tsvReader.getFieldNames(), "New field missing (i_TJ_Data_Who) from header")
ctrOut = 0
for lineDict in tsvReader:
ctrOut += 1
ctrIn = 0
for lineDict in tsvReaderIn:
ctrIn += 1
ctrIn += len(tsvReaderIn.getCommentsAsList())
ctrOut += len(tsvReader.getCommentsAsList())
self.assertTrue(ctrOut == (ctrIn + 2), "Output file should have same number of lines plus two (for maf version and Oncotator version comments) as input file. (In,Out): " + str(ctrIn) + ", " + str(ctrOut))
def testBasicDatasourceSorting(self):
"""Test that the GAF datasource is sorted before a gene-based datasource"""
gafDatasource = TestUtils.createTranscriptProviderDatasource(
self.config)
geneDS = DatasourceFactory.createDatasource(
"testdata/small_tsv_ds/small_tsv_ds.config",
"testdata/small_tsv_ds/")
incorrectSortList = [geneDS, gafDatasource]
guessSortList = DatasourceFactory.sortDatasources(incorrectSortList)
self.assertTrue(guessSortList[1] == geneDS, "Sorting is incorrect.")
self.assertTrue(
len(guessSortList) == 2,
"Sorting altered number of datasources (gt: 2): " +
str(len(guessSortList)))
def test_no_overwriting_muts(self):
"""Ensure that (given configuration that disallows) we cannot annotate from a datasource when a value was specified in the input."""
# We will have an input with a "Who" annotation that this datasource will try to write.
gene_ds = DatasourceFactory.createDatasource(
"testdata/thaga_janakari_gene_ds/hg19/tj_data.config", "testdata/thaga_janakari_gene_ds/hg19/"
)
input_filename = "testdata/maflite/who_alt1_vs_alt2.maflite"
output_filename = "out/who_alt1_vs_alt2.maf.annotated"
input_format = "MAFLITE"
output_format = "TCGAMAF"
other_opts = {OptionConstants.ALLOW_ANNOTATION_OVERWRITING: False, OptionConstants.NO_PREPEND: True}
run_spec = RunSpecificationFactory.create_run_spec_given_datasources(
input_format,
output_format,
input_filename,
output_filename,
datasource_list=[gene_ds],
other_opts=other_opts,
)
annotator = Annotator()
annotator.initialize(run_spec)
self.assertRaises(DuplicateAnnotationException, annotator.annotate)
def testBasicAnnotation(self):
''' Test annotation from a generic TSV based on a transcript annotation. Only confirms the proper headers of the output. '''
# We need a gaf data source to annotate gene
gafDatasource = TestUtils.createTranscriptProviderDatasource(
config=self.config)
transcriptDS = DatasourceFactory.createDatasource(
"testdata/small_transcript_tsv_ds/small_transcript_tsv_ds.config",
"testdata/small_transcript_tsv_ds/")
outputFilename = 'out/genericTranscriptTest.out.tsv'
annotator = Annotator()
annotator.setInputCreator(
MafliteInputMutationCreator(
'testdata/maflite/Patient0.snp.maf.txt'))
annotator.setOutputRenderer(SimpleOutputRenderer(outputFilename))
annotator.addDatasource(gafDatasource)
annotator.addDatasource(transcriptDS)
outputFilename = annotator.annotate()
tsvReader = GenericTsvReader(outputFilename)
headers = tsvReader.getFieldNames()
self.assertTrue(
"refseq_test_mRNA_Id" in headers,
"refseq_test_mRNA_Id not found in headers: " + str(headers))
self.assertTrue(
"refseq_test_prot_Id" in headers,
"refseq_test_prot_Id not found in headers: " + str(headers))
def createCosmicDatasource(config):
""" Creates a Cosmic datasource from a config file.
"""
cosmic_dirname = config.get("COSMIC", "CosmicDir")
cosmicDatasource = DatasourceFactory.createDatasource(
cosmic_dirname + "/cosmic.config", cosmic_dirname)
return cosmicDatasource
def test_overlapping_single_transcripts(self):
base_config_location = "testdata/ensembl/saccer/"
ensembl_ds = DatasourceFactory.createDatasource(base_config_location + "ensembl.config", base_config_location)
recs = ensembl_ds.get_overlapping_transcripts("I", "500", "500")
self.assertTrue(len(recs) == 1)
self.assertTrue(recs[0].get_gene() == 'YAL069W')
def testBasicAnnotation(self):
''' Annotate from a basic tsv of Genomic positions. This tests both single- and multiple-nucleotide variants. The tsv is already installed (i.e. proper config file created).
'''
outputFilename = 'out/genericGenomePositionTest.out.tsv'
gpDS = DatasourceFactory.createDatasource("testdata/small_genome_position_tsv_ds/oreganno_trim.config", "testdata/small_genome_position_tsv_ds/")
annotator = Annotator()
annotator.setInputCreator(MafliteInputMutationCreator('testdata/maflite/tiny_maflite.maf.txt'))
annotator.setOutputRenderer(SimpleOutputRenderer(outputFilename))
annotator.addDatasource(gpDS)
testFilename = annotator.annotate()
# Make sure that some values were populated
self.assertTrue(os.path.exists(testFilename))
tsvReader = GenericTsvReader(testFilename)
ctr = 1
# Two overlap, one does not. Repeat...
for lineDict in tsvReader:
if (ctr % 3 == 0):
self.assertTrue(lineDict["ORegAnno_hg19.oreganno.id"] == '', "Line " + str(ctr) + " should have had blank value, but did not: " + lineDict["ORegAnno_hg19.oreganno.id"])
else:
self.assertFalse(lineDict["ORegAnno_hg19.oreganno.id"] == '', "Line " + str(ctr) + " should not have had blank value, but did.")
self.assertTrue(lineDict["ORegAnno_hg19.oreganno.id"] == 'OREG0013034', "Line " + str(ctr) + " did not have correct value: " + lineDict["ORegAnno_hg19.oreganno.id"])
ctr = ctr + 1
def test_overwriting_muts(self):
"""Ensure that (given correct configuration) we can annotate from a datasource, even if the datasource will overwrite an existing mutation."""
# We will have an input with a "Who" annotation that this datasource will try to write.
gene_ds = DatasourceFactory.createDatasource(
"testdata/thaga_janakari_gene_ds/hg19/tj_data.config", "testdata/thaga_janakari_gene_ds/hg19/"
)
input_filename = "testdata/maflite/who_alt1_vs_alt2.maflite"
output_filename = "out/who_alt1_vs_alt2.maf.annotated"
input_format = "MAFLITE"
output_format = "TCGAMAF"
other_opts = {OptionConstants.ALLOW_ANNOTATION_OVERWRITING: True, OptionConstants.NO_PREPEND: True}
run_spec = RunSpecificationFactory.create_run_spec_given_datasources(
input_format,
output_format,
input_filename,
output_filename,
datasource_list=[gene_ds],
other_opts=other_opts,
)
annotator = Annotator()
annotator.initialize(run_spec)
annotator.annotate()
tsv_reader = GenericTsvReader(output_filename)
for i, line_dict in enumerate(tsv_reader):
self.assertTrue(line_dict.get("TJ_Data_Who", "") != "Tromokratis")
def testCreationAndAnnotation(self):
""" Test the datasource creation and then do a simple annotation
"""
outputFilename = 'out/genericGeneProteinPositionTest.out.tsv'
gafDS = TestUtils.createTranscriptProviderDatasource(self.config)
gppDS = DatasourceFactory.createDatasource("testdata/simple_uniprot_natvar/simple_uniprot_natvar.config", "testdata/simple_uniprot_natvar/")
annotator = Annotator()
annotator.setInputCreator(MafliteInputMutationCreator('testdata/maflite/tiny_maflite_natvar.maf.tsv'))
annotator.setOutputRenderer(SimpleOutputRenderer(outputFilename))
annotator.addDatasource(gafDS)
annotator.addDatasource(gppDS)
testFilename = annotator.annotate()
# Make sure that some values were populated
self.assertTrue(os.path.exists(testFilename))
tsvReader = GenericTsvReader(testFilename)
ctr = 0
for lineDict in tsvReader:
colName = "UniProt_NatVar_natural_variations"
self.assertTrue(sorted(lineDict[colName].split("|")) == sorted("R -> RR (in EDMD2).|R -> Q (in EDMD2).".split("|")), "Annotation value did not match: " + lineDict[colName])
ctr += 1
self.assertTrue(ctr == 1, "Number of mutations incorrect (1): " + str(ctr) )
def test_overlapping_single_transcripts(self):
base_config_location = "testdata/ensembl/saccer/"
ensembl_ds = DatasourceFactory.createDatasource(base_config_location + "ensembl.config", base_config_location)
recs = ensembl_ds.get_overlapping_transcripts("I", "500", "500")
self.assertTrue(len(recs) == 1)
self.assertTrue(recs[0].get_gene() == 'YAL069W')
def testMulticoreNoDatasources(self):
""" If using multicore, does not hang when no datasources are in the db dir"""
multiDS = DatasourceFactory.createDatasources('testdata/maflite/',
"hg19", True)
self.assertTrue(
len(multiDS) == 0,
"Length of multiDS when there were no datasources was not zero.")
def test_overwriting_muts(self):
"""Ensure that (given correct configuration) we can annotate from a datasource, even if the datasource will overwrite an existing mutation."""
# We will have an input with a "Who" annotation that this datasource will try to write.
gene_ds = DatasourceFactory.createDatasource(
"testdata/thaga_janakari_gene_ds/hg19/tj_data.config",
"testdata/thaga_janakari_gene_ds/hg19/")
input_filename = "testdata/maflite/who_alt1_vs_alt2.maflite"
output_filename = "out/who_alt1_vs_alt2.maf.annotated"
input_format = "MAFLITE"
output_format = "TCGAMAF"
other_opts = {
OptionConstants.ALLOW_ANNOTATION_OVERWRITING: True,
OptionConstants.NO_PREPEND: True
}
run_spec = RunSpecificationFactory.create_run_spec_given_datasources(
input_format,
output_format,
input_filename,
output_filename,
datasource_list=[gene_ds],
other_opts=other_opts)
annotator = Annotator()
annotator.initialize(run_spec)
annotator.annotate()
tsv_reader = GenericTsvReader(output_filename)
for i, line_dict in enumerate(tsv_reader):
self.assertTrue(line_dict.get('TJ_Data_Who', "") != "Tromokratis")
def testdbNSFPNoRefAltAnnotationWithExactMatch(self):
"""
"""
self.logger.info("Initializing dbNSFP")
tabixIndexedTsvDirName = os.path.join(*["testdata", "dbNSFP_chr1_chr3_100vars_exact_no_ref_alt_ds", "hg19"])
tabixIndexedTsvDatasource = DatasourceFactory.createDatasource(
os.path.join(tabixIndexedTsvDirName, "dbNSFP_chr1_chr3_100vars_exact_no_ref_alt_ds.config"),
tabixIndexedTsvDirName)
m1 = MutationData()
m1.chr = "1"
m1.start = "35140"
m1.end = "35140"
m1_annotated = tabixIndexedTsvDatasource.annotate_mutation(m1)
m1_annotation = m1_annotated.getAnnotation("dbNSFP_codonpos")
cur_annotation = Annotation(value="1|1|1", datasourceName="dbNSFP", dataType="String",
description="", tags=[TagConstants.INFO, TagConstants.NOT_SPLIT], number=None)
self.assertTrue(m1_annotation.isEqual(cur_annotation), "Annotations do not match.")
m1_annotation = m1_annotated.getAnnotation("dbNSFP_refcodon")
cur_annotation = Annotation(value="TAA|TAA|TAA", datasourceName="dbNSFP", dataType="String",
description="", tags=[TagConstants.INFO, TagConstants.NOT_SPLIT], number=None)
self.assertTrue(m1_annotation.isEqual(cur_annotation), "Annotations do not match.")
m1_annotation = m1_annotated.getAnnotation("dbNSFP_cds_strand")
cur_annotation = Annotation(value="-|-|-", datasourceName="dbNSFP", dataType="String",
description="", tags=[TagConstants.INFO, TagConstants.NOT_SPLIT], number=None)
self.assertTrue(m1_annotation.isEqual(cur_annotation), "Annotations do not match.")
def test_no_overwriting_muts(self):
"""Ensure that (given configuration that disallows) we cannot annotate from a datasource when a value was specified in the input."""
# We will have an input with a "Who" annotation that this datasource will try to write.
gene_ds = DatasourceFactory.createDatasource(
"testdata/thaga_janakari_gene_ds/hg19/tj_data.config",
"testdata/thaga_janakari_gene_ds/hg19/")
input_filename = "testdata/maflite/who_alt1_vs_alt2.maflite"
output_filename = "out/who_alt1_vs_alt2.maf.annotated"
input_format = "MAFLITE"
output_format = "TCGAMAF"
other_opts = {
OptionConstants.ALLOW_ANNOTATION_OVERWRITING: False,
OptionConstants.NO_PREPEND: True
}
run_spec = RunSpecificationFactory.create_run_spec_given_datasources(
input_format,
output_format,
input_filename,
output_filename,
datasource_list=[gene_ds],
other_opts=other_opts)
annotator = Annotator()
annotator.initialize(run_spec)
self.assertRaises(DuplicateAnnotationException, annotator.annotate)
def testAnnotateListOfMutations(self):
"""Test that we can initialize an Annotator, without an input or output and then feed mutations,
one at a time... using a runspec"""
# Locate the datasource directory and create a runspec
dbDir = self.config.get("DEFAULT", "dbDir")
ds = DatasourceFactory.createDatasources(dbDir)
runSpec = RunSpecification()
runSpec.initialize(None, None, datasources=ds)
# Initialize the annotator with the runspec
annotator = Annotator()
annotator.initialize(runSpec)
m = MutationData()
m.chr = "1"
m.start = "12941796"
m.end = "12941796"
m.alt_allele = "G"
m.ref_allele = "T"
muts = [m]
muts = annotator.annotate_mutations(muts)
m2 = muts.next()
self.assertTrue(m2.get("gene", None) is not None)
def testCreationAndAnnotation(self):
""" Test the datasource creation and then do a simple annotation
"""
outputFilename = 'out/genericGeneProteinPositionTest.out.tsv'
gafDS = TestUtils.createTranscriptProviderDatasource(self.config)
gppDS = DatasourceFactory.createDatasource("testdata/simple_uniprot_natvar/simple_uniprot_natvar.config", "testdata/simple_uniprot_natvar/")
annotator = Annotator()
annotator.setInputCreator(MafliteInputMutationCreator('testdata/maflite/tiny_maflite_natvar.maf.tsv'))
annotator.setOutputRenderer(SimpleOutputRenderer(outputFilename))
annotator.addDatasource(gafDS)
annotator.addDatasource(gppDS)
testFilename = annotator.annotate()
# Make sure that some values were populated
self.assertTrue(os.path.exists(testFilename))
tsvReader = GenericTsvReader(testFilename)
ctr = 0
for lineDict in tsvReader:
colName = "UniProt_NatVar_natural_variations"
self.assertTrue(sorted(lineDict[colName].split("|")) == sorted("R -> RR (in EDMD2).|R -> Q (in EDMD2).".split("|")), "Annotation value did not match: " + lineDict[colName])
ctr += 1
self.assertTrue(ctr == 1, "Number of mutations incorrect (1): " + str(ctr) )
def testdbNSFPAnnotationWithMissingOverlapMatch(self): # SNPs only
"""
"""
self.logger.info("Initializing dbNSFP")
tabixIndexedTsvDirName = os.path.join(*["testdata", "dbNSFP_chr1_chr3_100vars_overlap_ds", "hg19"])
tabixIndexedTsvDatasource = DatasourceFactory.createDatasource(
os.path.join(tabixIndexedTsvDirName, "dbNSFP_chr1_chr3_100vars_overlap_ds.config"), tabixIndexedTsvDirName)
m1 = MutationDataFactory.default_create()
m1.chr = "1"
m1.start = "35136"
m1.end = "35137"
m1_annotated = tabixIndexedTsvDatasource.annotate_mutation(m1)
m1_annotation = m1_annotated.getAnnotation("dbNSFP_codonpos")
cur_annotation = Annotation(value="", datasourceName="dbNSFP", dataType="String",
description="", tags=[TagConstants.INFO, TagConstants.NOT_SPLIT], number=None)
self.assertTrue(m1_annotation.isEqual(cur_annotation), "Annotations do not match.")
m1_annotation = m1_annotated.getAnnotation("dbNSFP_refcodon")
cur_annotation = Annotation(value="", datasourceName="dbNSFP", dataType="String",
description="", tags=[TagConstants.INFO, TagConstants.NOT_SPLIT], number=None)
self.assertTrue(m1_annotation.isEqual(cur_annotation), "Annotations do not match.")
m1_annotation = m1_annotated.getAnnotation("dbNSFP_cds_strand")
cur_annotation = Annotation(value="", datasourceName="dbNSFP", dataType="String",
description="", tags=[TagConstants.INFO, TagConstants.NOT_SPLIT], number=None)
self.assertTrue(m1_annotation.isEqual(cur_annotation), "Annotations do not match.")
def testESPCoverageAnnotationWithSNPAvgMatch(self):
"""
"""
self.logger.info("Initializing ESP6500SI-V2 Coverage")
tabixIndexedTsvDirName = os.path.join(*["testdata", "small_esp_coverage_avg_ds", "hg19"])
tabixIndexedTsvDatasource = DatasourceFactory.createDatasource(
os.path.join(tabixIndexedTsvDirName, "small_esp_coverage_avg_ds.config"), tabixIndexedTsvDirName)
m1 = MutationData()
m1.chr = "X"
m1.start = "100075334"
m1.end = "100075334"
m1_annotated = tabixIndexedTsvDatasource.annotate_mutation(m1)
m1_annotation = m1_annotated.getAnnotation("ESP_AvgAAsampleReadDepth")
cur_annotation = Annotation(value="75.0", datasourceName="ESP", dataType="Float",
description="", tags=[TagConstants.INFO, TagConstants.NOT_SPLIT], number=None)
self.assertTrue(m1_annotation.isEqual(cur_annotation), "Annotations do not match.")
m1_annotation = m1_annotated.getAnnotation("ESP_TotalAAsamplesCovered")
cur_annotation = Annotation(value="692.0", datasourceName="ESP", dataType="Float",
description="", tags=[TagConstants.INFO, TagConstants.NOT_SPLIT], number=None)
self.assertTrue(m1_annotation.isEqual(cur_annotation), "Annotations do not match.")
m1_annotation = m1_annotated.getAnnotation("ESP_Chromosome")
cur_annotation = Annotation(value="X", datasourceName="ESP", dataType="String",
description="", tags=[TagConstants.INFO, TagConstants.NOT_SPLIT], number=None)
self.assertTrue(m1_annotation.isEqual(cur_annotation), "Annotations do not match.")
def testExampleVcfDBAnnotationWithSNPExactMatch(self):
"""
"""
tabixIndexedVcfDirName = os.path.join(*["testdata", "vcf_db_exact", "hg19"])
tabixIndexedVcfDatasource = DatasourceFactory.createDatasource(
os.path.join(tabixIndexedVcfDirName, "vcf_db_exact.config"), tabixIndexedVcfDirName)
chrom = "20"
start = "1110696"
end = "1110696"
ref_allele = "A"
alt_allele = "T"
build = "hg19"
m1 = MutUtils.initializeMutFromAttributes(chrom, start, end, ref_allele, alt_allele, build)
m1_annotated = tabixIndexedVcfDatasource.annotate_mutation(m1)
m1_annotation = m1_annotated.getAnnotation("ESP_AF")
cur_annotation = Annotation(value="0.667", datasourceName="ESP", dataType="Float",
description="Allele Frequency", tags=[TagConstants.INFO, TagConstants.SPLIT],
number=-1)
self.assertTrue(m1_annotation.isEqual(cur_annotation), "Annotations do not match.")
m1_annotation = m1_annotated.getAnnotation("ESP_AC")
cur_annotation = Annotation(value="2,4", datasourceName="ESP", dataType="Integer",
description="Allele Count", tags=[TagConstants.INFO, TagConstants.NOT_SPLIT],
number=None)
self.assertTrue(m1_annotation.isEqual(cur_annotation), "Annotations do not match.")
m1_annotation = m1_annotated.getAnnotation("ESP_H2")
cur_annotation = Annotation(value="False", datasourceName="ESP", dataType="Flag",
description="HapMap2 membership", tags=[TagConstants.INFO, TagConstants.NOT_SPLIT],
number=0)
self.assertTrue(m1_annotation.isEqual(cur_annotation), "Annotations do not match.")
chrom = "20"
start = "1230237"
end = "1230237"
ref_allele = "T"
alt_allele = "A"
build = "hg19"
m1 = MutUtils.initializeMutFromAttributes(chrom, start, end, ref_allele, alt_allele, build)
m1_annotated = tabixIndexedVcfDatasource.annotate_mutation(m1)
m1_annotation = m1_annotated.getAnnotation("ESP_NS")
cur_annotation = Annotation(value="3", datasourceName="ESP", dataType="Integer",
description="Number of Samples With Data",
tags=[TagConstants.INFO, TagConstants.NOT_SPLIT],
number=1)
self.assertTrue(m1_annotation.isEqual(cur_annotation), "Annotations do not match.")
m1_annotation = m1_annotated.getAnnotation("ESP_AF")
cur_annotation = Annotation(value="", datasourceName="ESP", dataType="Float",
description="Allele Frequency", tags=[TagConstants.INFO, TagConstants.SPLIT],
number=-1)
self.assertTrue(m1_annotation.isEqual(cur_annotation), "Annotations do not match.")
def test_hashcode_generation(self):
"""Test that we can read a hashcode for a datasource, if available."""
geneDS = DatasourceFactory.createDatasource(
"testdata/thaga_janakari_gene_ds/hg19/tj_data.config",
"testdata/thaga_janakari_gene_ds/hg19/")
self.assertTrue(geneDS is not None,
"gene indexed datasource was None.")
self.assertTrue(
geneDS.get_hashcode() == "7120edfdc7b29e45191c81c99894afd5")
def testBasicGeneTSVInit(self):
""" Make sure that we can initialize a simple tsv data source """
geneDS = DatasourceFactory.createDatasource("testdata/small_tsv_ds/small_tsv_ds.config", "testdata/small_tsv_ds/")
self.assertTrue(geneDS <> None, "gene indexed datasource was None.")
m = MutationDataFactory.default_create()
m.createAnnotation('gene',"ABL1")
m = geneDS.annotate_mutation(m)
self.assertTrue(m['CGC_Abridged_Name'] == "v-abl Abelson murine leukemia viral oncogene homolog 1","Test gene TSV datasource did not annotate properly.")
def testBasicAnnotation(self):
''' Annotate from a basic tsv gene file. Use the Gaf to annotate before trying the tsv -- required since the gene annotation must be populated.
Using trimmed CancerGeneCensus as basis for this test.
'''
# cut -f 1 oncotator/test/testdata/small_tsv_ds/CancerGeneCensus_Table_1_full_2012-03-15_trim.txt | egrep -v Symbol | sed -r "s/^/'/g" | sed ':a;N;$!ba;s/\n/,/g' | sed -r "s/,'/','/g"
genesAvailable = [
'ABL1', 'ABL2', 'ACSL3', 'AF15Q14', 'AF1Q', 'AF3p21', 'AF5q31',
'AKAP9', 'AKT1', 'AKT2', 'ALDH2', 'ALK', 'ALO17', 'APC',
'ARHGEF12', 'ARHH', 'ARID1A', 'ARID2', 'ARNT', 'ASPSCR1', 'ASXL1',
'ATF1', 'ATIC', 'ATM', 'ATRX', 'BAP1', 'BCL10', 'BCL11A', 'BCL11B'
]
# We need a gaf data source to annotate gene
gafDatasource = TestUtils.createTranscriptProviderDatasource(
config=self.config)
geneDS = DatasourceFactory.createDatasource(
"testdata/small_tsv_ds/small_tsv_ds.config",
"testdata/small_tsv_ds/")
outputFilename = 'out/genericGeneTest.out.tsv'
annotator = Annotator()
annotator.setInputCreator(
MafliteInputMutationCreator(
'testdata/maflite/Patient0.snp.maf.txt'))
annotator.setOutputRenderer(SimpleOutputRenderer(outputFilename))
annotator.addDatasource(gafDatasource)
annotator.addDatasource(geneDS)
annotator.annotate()
# Check that there were actual annotations performed.
tsvReader = GenericTsvReader(outputFilename)
fields = tsvReader.getFieldNames()
self.assertTrue(
'CGC_Abridged_Other Syndrome/Disease' in fields,
"'CGC_Other Syndrome/Disease' was not present in the header")
self.assertTrue(
'CGC_Abridged_Mutation Type' in fields,
"'CGC_Abridged_Mutation Type' was not present in the header")
ctr = 1
linesThatShouldBeAnnotated = 0
for lineDict in tsvReader:
self.assertTrue('gene' in lineDict.keys())
if lineDict['gene'] in genesAvailable:
self.assertTrue(
lineDict['CGC_Abridged_GeneID'] != '',
"'CGC_Abridged_GeneID' was missing on a row that should have been populated. Line: "
+ str(ctr))
linesThatShouldBeAnnotated += 1
ctr += 1
self.assertTrue((linesThatShouldBeAnnotated) > 0,
"Bad data -- cannot test missed detects.")
def test_simple_transcript_annotation(self):
"""Test web api backend call /transcript/ """
# http://www.broadinstitute.org/oncotator/transcript/ENST00000215832.6/
datasource_list = DatasourceFactory.createDatasources(self._determine_db_dir(), "hg19", isMulticore=False)
annotator = Annotator()
for ds in datasource_list:
annotator.addDatasource(ds)
tx = annotator.retrieve_transcript_by_id("ENST00000215832.6")
self.assertTrue(tx is not None)
self.assertTrue(tx.get_gene() == "MAPK1")
def test_querying_transcripts_by_genes(self):
"""Test that we can get all of the transcripts for a given set of genes. """
datasource_list = DatasourceFactory.createDatasources(self._determine_db_dir(), "hg19", isMulticore=False)
annotator = Annotator()
for ds in datasource_list:
annotator.addDatasource(ds)
# Step 1 get all of the relevant transcripts
txs = annotator.retrieve_transcripts_by_genes(["MAPK1", "PIK3CA"])
self.assertTrue(len(txs) > 3)
def testAnnotationSourceIsPopulated(self):
''' Tests that the annotation source is not blank for the example tsv datasource. '''
geneDS = DatasourceFactory.createDatasource("testdata/small_tsv_ds/small_tsv_ds.config", "testdata/small_tsv_ds/")
self.assertTrue(geneDS <> None, "gene indexed datasource was None.")
m = MutationData()
m.createAnnotation('gene',"ABL1")
m = geneDS.annotate_mutation(m)
self.assertTrue(m['CGC_Abridged_Name'] == "v-abl Abelson murine leukemia viral oncogene homolog 1","Test gene TSV datasource did not annotate properly.")
self.assertTrue(m.getAnnotation('CGC_Abridged_Name').getDatasource() <> "Unknown", "Annotation source was unknown")
self.assertTrue(m.getAnnotation('CGC_Abridged_Name').getDatasource().strip() <> "", "Annotation source was blank")
def testDatasourceCreator(self):
""" Test that the datasource creator process will work for TranscriptToUniProtProteinPositionTransformingDatasource. NOTE: This test needs to be updated to use sqlite instead of filesystem file.
"""
tDS = DatasourceFactory.createDatasource("testdata/small_uniprot_prot_seq_ds/small_uniprot_prot_seq_ds.config", "testdata/small_uniprot_prot_seq_ds/")
outputAnnotation = "UniProt_aapos"
m = MutationData()
m.createAnnotation('transcript_id', 'uc009vvt.1')
m.createAnnotation('protein_change', 'p.T1105A')
m = tDS.annotate_mutation(m)
self.assertTrue(m[outputAnnotation] == "969", "Did not get proper value (969): " + m[outputAnnotation])
def test_overlapping_multiple_transcripts_snp(self):
base_config_location = "testdata/ensembl/saccer/"
ensembl_ds = DatasourceFactory.createDatasource(base_config_location + "ensembl.config", base_config_location)
recs = ensembl_ds.get_overlapping_transcripts("I", "550", "550")
self.assertTrue(len(recs) == 2)
ids = set()
for r in recs:
ids.add(r.get_transcript_id())
self.assertTrue(len(ids - {'YAL069W', 'YAL068W-A'}) == 0)
def test_querying_transcripts_by_genes(self):
"""Test that we can get all of the transcripts for a given set of genes. """
datasource_list = DatasourceFactory.createDatasources(self._determine_db_dir(), "hg19", isMulticore=False)
annotator = Annotator()
for ds in datasource_list:
annotator.addDatasource(ds)
# Step 1 get all of the relevant transcripts
txs = annotator.retrieve_transcripts_by_genes(["MAPK1", "PIK3CA"])
self.assertTrue(len(txs) > 3)
def test_simple_transcript_annotation(self):
"""Test web api backend call /transcript/ """
# http://www.broadinstitute.org/oncotator/transcript/ENST00000215832.6/
datasource_list = DatasourceFactory.createDatasources(self._determine_db_dir(), "hg19", isMulticore=False)
annotator = Annotator()
for ds in datasource_list:
annotator.addDatasource(ds)
tx = annotator.retrieve_transcript_by_id("ENST00000215832.6")
self.assertTrue(tx is not None)
self.assertTrue(tx.get_gene() == "MAPK1")
def test_overlapping_multiple_transcripts_snp(self):
base_config_location = "testdata/ensembl/saccer/"
ensembl_ds = DatasourceFactory.createDatasource(base_config_location + "ensembl.config", base_config_location)
recs = ensembl_ds.get_overlapping_transcripts("I", "550", "550")
self.assertTrue(len(recs) == 2)
ids = set()
for r in recs:
ids.add(r.get_transcript_id())
self.assertTrue(len(ids - set(['YAL069W', 'YAL068W-A'])) == 0)
def testAnnotationSourceIsPopulated(self):
''' Tests that the annotation source is not blank for the example tsv datasource. '''
geneDS = DatasourceFactory.createDatasource("testdata/small_tsv_ds/small_tsv_ds.config", "testdata/small_tsv_ds/")
self.assertTrue(geneDS <> None, "gene indexed datasource was None.")
m = MutationData()
m.createAnnotation('gene',"ABL1")
m = geneDS.annotate_mutation(m)
self.assertTrue(m['CGC_Abridged_Name'] == "v-abl Abelson murine leukemia viral oncogene homolog 1","Test gene TSV datasource did not annotate properly.")
self.assertTrue(m.getAnnotation('CGC_Abridged_Name').getDatasource() <> "Unknown", "Annotation source was unknown")
self.assertTrue(m.getAnnotation('CGC_Abridged_Name').getDatasource().strip() <> "", "Annotation source was blank")
def testdbNSFPAnnotationWithMissingExactMatch(self): # SNPs only
"""
"""
self.logger.info("Initializing dbNSFP")
tabixIndexedTsvDirName = os.path.join(
*["testdata", "dbNSFP_chr1_6vars_exact_ds", "hg19"])
tabixIndexedTsvDatasource = DatasourceFactory.createDatasource(
os.path.join(tabixIndexedTsvDirName,
"dbNSFP_chr1_6vars_exact_ds.config"),
tabixIndexedTsvDirName)
m1 = MutationData()
m1.chr = "1"
m1.start = "35138"
m1.end = "35138"
m1.ref_allele = "T"
m1.alt_allele = "C"
m1_annotated = tabixIndexedTsvDatasource.annotate_mutation(m1)
m1_annotation = m1_annotated.getAnnotation("dbNSFP_codonpos")
cur_annotation = Annotation(
value="",
datasourceName="dbNSFP",
dataType="Integer",
description="",
tags=[TagConstants.INFO, TagConstants.NOT_SPLIT],
number=None)
self.assertTrue(m1_annotation.isEqual(cur_annotation),
"Annotations do not match.")
m1_annotation = m1_annotated.getAnnotation("dbNSFP_refcodon")
cur_annotation = Annotation(
value="",
datasourceName="dbNSFP",
dataType="String",
description="",
tags=[TagConstants.INFO, TagConstants.NOT_SPLIT],
number=None)
self.assertTrue(m1_annotation.isEqual(cur_annotation),
"Annotations do not match.")
m1_annotation = m1_annotated.getAnnotation("dbNSFP_cds_strand")
cur_annotation = Annotation(
value="",
datasourceName="dbNSFP",
dataType="Float",
description="",
tags=[TagConstants.INFO, TagConstants.NOT_SPLIT],
number=None)
self.assertTrue(m1_annotation.isEqual(cur_annotation),
"Annotations do not match.")
def testdbNSFPNoRefAltAnnotationWithExactMatch(self):
"""
"""
self.logger.info("Initializing dbNSFP")
tabixIndexedTsvDirName = os.path.join(*[
"testdata", "dbNSFP_chr1_chr3_100vars_exact_no_ref_alt_ds", "hg19"
])
tabixIndexedTsvDatasource = DatasourceFactory.createDatasource(
os.path.join(
tabixIndexedTsvDirName,
"dbNSFP_chr1_chr3_100vars_exact_no_ref_alt_ds.config"),
tabixIndexedTsvDirName)
m1 = MutationDataFactory.default_create()
m1.chr = "1"
m1.start = "35140"
m1.end = "35140"
m1_annotated = tabixIndexedTsvDatasource.annotate_mutation(m1)
m1_annotation = m1_annotated.getAnnotation("dbNSFP_codonpos")
cur_annotation = Annotation(
value="1|1|1",
datasourceName="dbNSFP",
dataType="String",
description="",
tags=[TagConstants.INFO, TagConstants.NOT_SPLIT],
number=None)
self.assertTrue(m1_annotation.isEqual(cur_annotation),
"Annotations do not match.")
m1_annotation = m1_annotated.getAnnotation("dbNSFP_refcodon")
cur_annotation = Annotation(
value="TAA|TAA|TAA",
datasourceName="dbNSFP",
dataType="String",
description="",
tags=[TagConstants.INFO, TagConstants.NOT_SPLIT],
number=None)
self.assertTrue(m1_annotation.isEqual(cur_annotation),
"Annotations do not match.")
m1_annotation = m1_annotated.getAnnotation("dbNSFP_cds_strand")
cur_annotation = Annotation(
value="-|-|-",
datasourceName="dbNSFP",
dataType="String",
description="",
tags=[TagConstants.INFO, TagConstants.NOT_SPLIT],
number=None)
self.assertTrue(m1_annotation.isEqual(cur_annotation),
"Annotations do not match.")
def test_simple_genes_by_gene_annotation(self):
"""Test web api backend call /gene/ """
# http://www.broadinstitute.org/oncotator/gene/MAPK1/
datasource_list = DatasourceFactory.createDatasources(self._determine_db_dir(), "hg19", isMulticore=False)
annotator = Annotator()
for ds in datasource_list:
annotator.addDatasource(ds)
txs = annotator.retrieve_transcripts_by_genes(["MAPK1"])
self.assertTranscriptsFound(txs)
mut_dict = annotator.annotate_genes_given_txs(txs)
self.assertTrue(len(mut_dict.keys()) == 1)
def test_simple_genes_by_gene_annotation(self):
"""Test web api backend call /gene/ """
# http://www.broadinstitute.org/oncotator/gene/MAPK1/
datasource_list = DatasourceFactory.createDatasources(self._determine_db_dir(), "hg19", isMulticore=False)
annotator = Annotator()
for ds in datasource_list:
annotator.addDatasource(ds)
txs = annotator.retrieve_transcripts_by_genes(["MAPK1"])
self.assertTranscriptsFound(txs)
mut_dict = annotator.annotate_genes_given_txs(txs)
self.assertTrue(len(mut_dict.keys()) == 1)
def testESPCoverageAnnotationWithMissingIndelOverlapMatch(self):
"""
"""
self.logger.info("Initializing ESP6500SI-V2 Coverage")
tabixIndexedTsvDirName = os.path.join(
*["testdata", "small_esp_coverage_overlap_ds", "hg19"])
tabixIndexedTsvDatasource = DatasourceFactory.createDatasource(
os.path.join(tabixIndexedTsvDirName,
"small_esp_coverage_overlap_ds.config"),
tabixIndexedTsvDirName)
m1 = MutationData()
m1.chr = "X"
m1.start = "100075300"
m1.end = "100075336"
m1_annotated = tabixIndexedTsvDatasource.annotate_mutation(m1)
m1_annotation = m1_annotated.getAnnotation("ESP_AvgAAsampleReadDepth")
cur_annotation = Annotation(
value="75.0|81.0|81.0",
datasourceName="ESP",
dataType="String",
description="",
tags=[TagConstants.INFO, TagConstants.NOT_SPLIT],
number=None)
self.assertTrue(m1_annotation.isEqual(cur_annotation),
"Annotations do not match.")
m1_annotation = m1_annotated.getAnnotation("ESP_TotalAAsamplesCovered")
cur_annotation = Annotation(
value="692|692|692",
datasourceName="ESP",
dataType="String",
description="",
tags=[TagConstants.INFO, TagConstants.NOT_SPLIT],
number=None)
self.assertTrue(m1_annotation.isEqual(cur_annotation),
"Annotations do not match.")
m1_annotation = m1_annotated.getAnnotation("ESP_Chromosome")
cur_annotation = Annotation(
value="X|X|X",
datasourceName="ESP",
dataType="String",
description="",
tags=[TagConstants.INFO, TagConstants.NOT_SPLIT],
number=None)
self.assertTrue(m1_annotation.isEqual(cur_annotation),
"Annotations do not match.")
def testBasicCosmicInit(self):
""" Very simple test that will create a datasource from a sample datasource directory.
The directory conforms to the standard datasource structure, including placement of the config file.
"""
ds = DatasourceFactory.createDatasource('testdata/small_cosmic/small_cosmic.config', "testdata/small_cosmic")
m = MutationDataFactory.default_create()
m.chr = 19
m.start = 58858921
m.end = 58858921
m = ds.annotate_mutation(m)
self.assertTrue(m['COSMIC_overlapping_mutation_AAs'] == 'p.P426P(1)', "Did not properly annotate mutation: " + m['COSMIC_overlapping_mutation_AAs'])
def testInitializingDatasources(self):
""" Test initializing a database dir, both single and multicore. This test is RAM intensive and requires default data corpus."""
multiDS = DatasourceFactory.createDatasources(self.config.get("DEFAULT", "dbDir"), "hg19", isMulticore=True)
self.assertTrue(multiDS is not None, "Datasource list was None")
self.assertTrue(len(multiDS) != 0, "Datasource list was empty")
for i in range(0,len(multiDS)):
self.assertTrue(multiDS[i] is not None, "multi core datasource was None: " + str(i))
self.assertTrue(isinstance(multiDS[i],Datasource))
# This test can be memory intensive, so get rid of the multiDS, but record how many datasources were created.
numMultiDS = len(multiDS)
del multiDS
singleCoreDS = DatasourceFactory.createDatasources(self.config.get("DEFAULT", "dbDir"), "hg19", isMulticore=False)
self.assertTrue(singleCoreDS is not None, "Datasource list was None")
self.assertTrue(len(singleCoreDS) != 0, "Datasource list was empty")
for i in range(0,len(singleCoreDS)):
self.assertTrue(singleCoreDS[i] is not None, "single core datasource was None: " + str(i))
self.assertTrue(isinstance(singleCoreDS[i],Datasource))
self.assertTrue(numMultiDS == len(singleCoreDS), "Length of single core datasource list was not the same as multicore")
del singleCoreDS
def test_simple_genes_by_region_annotation(self):
"""Test web api backend call /genes/ """
# http://www.broadinstitute.org/oncotator/genes/chr22_22112223_22312558/
# Two genes: chr22:22,112,223-22,312,558
datasource_list = DatasourceFactory.createDatasources(self._determine_db_dir(), "hg19", isMulticore=False)
annotator = Annotator()
for ds in datasource_list:
annotator.addDatasource(ds)
# Here is what the API would call....
txs = annotator.retrieve_transcripts_by_region("22", 22112223, 22312558)
self.assertTranscriptsFound(txs)
mut_dict = annotator.annotate_genes_given_txs(txs)
# Each mut will be for a separate gene
for gene in mut_dict.keys():
mut = mut_dict[gene]
alt_accessions = mut["UniProt_alt_uniprot_accessions"].split("|")
tcgascape_amp_peaks = mut["TCGAScape_Amplification_Peaks"].split("|")
tcgascape_del_peaks = mut["TCGAScape_Deletion_Peaks"].split("|")
tumorscape_amp_peaks = mut["TUMORScape_Amplification_Peaks"].split("|")
tumorscape_del_peaks = mut["TUMORScape_Deletion_Peaks"].split("|")
full_name = mut["HGNC_Approved Name"]
cosmic = {
"tissue_types_affected": mut["COSMIC_Tissue_tissue_types_affected"],
"total_alterations_in_gene": mut["COSMIC_Tissue_tissue_types_affected"],
}
alt_aliases = list(
itertools.chain([mut["HGNC_Previous Symbols"].split(", "), mut["HGNC_Synonyms"].split(", ")])
)
location = mut["HGNC_Chromosome"]
uniprot_accession = mut["UniProt_uniprot_accession"]
transcripts = mut["transcripts"]
self.assertTrue(transcripts is not None)
self.assertTrue(len(transcripts) > 0)
self.assertTrue(transcripts.startswith("ENST"))
strand = mut["strand"]
klass = mut["class"]
uniprot_experimentals = mut["UniProt_AA_experimental_info"].split("|")
self.assertTrue(uniprot_experimentals is not None)
uniprot_natural_variations = mut["UniProt_AA_natural_variation"].split("|")
uniprot_regions = mut["UniProt_AA_region"].split("|")
uniprot_sites = mut["UniProt_AA_site"].split("|")
uniprot_go_biological_processes = mut["UniProt_GO_Biological_Process"].split("|")
uniprot_go_cellular_components = mut["UniProt_GO_Cellular_Component"].split("|")
self.assertTrue(uniprot_go_cellular_components is not None)
uniprot_go_molecular_functions = mut["UniProt_GO_Molecular_Function"].split("|")
pass
def testBasicGeneTSVInit(self):
""" Make sure that we can initialize a simple tsv data source """
geneDS = DatasourceFactory.createDatasource(
"testdata/small_tsv_ds/small_tsv_ds.config",
"testdata/small_tsv_ds/")
self.assertTrue(geneDS <> None, "gene indexed datasource was None.")
m = MutationDataFactory.default_create()
m.createAnnotation('gene', "ABL1")
m = geneDS.annotate_mutation(m)
self.assertTrue(
m['CGC_Abridged_Name'] ==
"v-abl Abelson murine leukemia viral oncogene homolog 1",
"Test gene TSV datasource did not annotate properly.")
def testTags(self):
"""
"""
self.logger.info("Initializing ESP6500SI-V2")
tabixIndexedVcfDirName = os.path.join(*["testdata", "small_esp_ds"])
tabixIndexedVcfDatasource = DatasourceFactory.createDatasource(
os.path.join(tabixIndexedVcfDirName, "esp.config"), tabixIndexedVcfDirName)
tagsDict = tabixIndexedVcfDatasource._determine_tags()
for ID in tagsDict:
tags = tagsDict[ID]
self.assertTrue(len(tags) == 2, "The length of tags is not 2 but %s." % len(tags))
self.assertTrue(TagConstants.INFO in tags, "INFO tag is missing for %s." % ID)
self.assertTrue(TagConstants.NOT_SPLIT in tags, "NOT_SPLIT tag is missing for %s." % ID)
def testDatasourceCreator(self):
""" Test that the datasource creator process will work for v1 of TranscriptToUniProtProteinPositionTransformingDatasource. NOTE: This test needs to be updated to use sqlite instead of filesystem file.
"""
tDS = DatasourceFactory.createDatasource(
"testdata/small_uniprot_prot_seq_ds/small_uniprot_prot_seq_ds.config",
"testdata/small_uniprot_prot_seq_ds/")
outputAnnotation = "UniProt_aapos"
m = MutationData()
m.createAnnotation('transcript_id', 'uc009vvt.1')
m.createAnnotation('protein_change', 'p.T1105A')
m = tDS.annotate_mutation(m)
self.assertTrue(
m[outputAnnotation] == "969",
"Did not get proper value (969): " + m[outputAnnotation])
def testSimpleAnnotation(self):
""" Create a dummy mutation and make sure it gets annotated properly """
m = MutationData()
m.createAnnotation("transcript_id", "uc001hms.3")
transcriptDS = DatasourceFactory.createDatasource(
"testdata/small_transcript_tsv_ds/small_transcript_tsv_ds.config", "testdata/small_transcript_tsv_ds/"
)
m = transcriptDS.annotate_mutation(m)
self.assertTrue(
m["refseq_test_mRNA_Id"] == "NM_022746",
"Transcript-based annotation did not populate properly: " + m["refseq_test_mRNA_Id"],
)
self.assertTrue(
m["refseq_test_prot_Id"] == "NP_073583",
"Transcript-based annotation did not populate properly: " + m["refseq_test_prot_Id"],
)
def test_simple_annotation_with_version_number_in_data_but_not_query(self):
""" Create a dummy mutation and make sure it gets annotated properly with version num in data, but not query """
m = MutationDataFactory.default_create()
m.createAnnotation("transcript_id", "uc001hms")
transcriptDS = DatasourceFactory.createDatasource(
"testdata/small_transcript_tsv_ds/small_transcript_tsv_ds.config", "testdata/small_transcript_tsv_ds/"
)
m = transcriptDS.annotate_mutation(m)
self.assertTrue(
m["refseq_test_mRNA_Id"] == "NM_022746",
"Transcript-based annotation did not populate properly: " + m["refseq_test_mRNA_Id"],
)
self.assertTrue(
m["refseq_test_prot_Id"] == "NP_073583",
"Transcript-based annotation did not populate properly: " + m["refseq_test_prot_Id"],
)
def testSimpleAnnotation(self):
''' Create a dummy mutation and make sure it gets annotated properly '''
m = MutationData()
m.createAnnotation('transcript_id', 'uc001hms.3')
transcriptDS = DatasourceFactory.createDatasource(
"testdata/small_transcript_tsv_ds/small_transcript_tsv_ds.config",
"testdata/small_transcript_tsv_ds/")
m = transcriptDS.annotate_mutation(m)
self.assertTrue(
m['refseq_test_mRNA_Id'] == 'NM_022746',
"Transcript-based annotation did not populate properly: " +
m['refseq_test_mRNA_Id'])
self.assertTrue(
m['refseq_test_prot_Id'] == 'NP_073583',
"Transcript-based annotation did not populate properly: " +
m['refseq_test_prot_Id'])
def test_simple_annotation_without_version_number_in_data_nor_query(self):
''' Create a dummy mutation and make sure it gets annotated properly when there is a version number in the query, but version number is not in the datasource.'''
m = MutationDataFactory.default_create()
m.createAnnotation('transcript_id', 'uc001hms')
transcriptDS = DatasourceFactory.createDatasource(
"testdata/small_transcript_tsv_ds_no_version_number/small_transcript_tsv_ds.config",
"testdata/small_transcript_tsv_ds_no_version_number/")
m = transcriptDS.annotate_mutation(m)
self.assertTrue(
m['refseq_test_mRNA_Id'] == 'NM_022746',
"Transcript-based annotation did not populate properly: " +
m['refseq_test_mRNA_Id'])
self.assertTrue(
m['refseq_test_prot_Id'] == 'NP_073583',
"Transcript-based annotation did not populate properly: " +
m['refseq_test_prot_Id'])
def testDoubleAnnotationError(self):
''' Given a maf file that used to cause a duplicate annotation exception, do not throw that (or any) exception. '''
outputFilename = 'out/genericGenomePositionDoubleAnnotationTest.out.tsv'
gpDS = DatasourceFactory.createDatasource("testdata/small_genome_position_tsv_ds/oreganno_trim.config", "testdata/small_genome_position_tsv_ds/")
annotator = Annotator()
annotator.setInputCreator(MafliteInputMutationCreator('testdata/maflite/testDoubleAnnotate.maf.tsv'))
annotator.setOutputRenderer(SimpleOutputRenderer(outputFilename))
annotator.addDatasource(gpDS)
testFilename = annotator.annotate()
# Make sure that some values were populated
self.assertTrue(os.path.exists(testFilename))
def testExampleVcfDBAnnotationWithMissingIndelExactMatch(self):
"""
"""
tabixIndexedVcfDirName = os.path.join(*["testdata", "vcf_db_exact", "hg19"])
tabixIndexedVcfDatasource = DatasourceFactory.createDatasource(
os.path.join(tabixIndexedVcfDirName, "vcf_db_exact.config"), tabixIndexedVcfDirName)
chrom = "21"
start = "1234567"
end = "1234567"
ref_allele = "AGTC"
alt_allele = "A"
build = "hg19"
m1 = MutUtils.initializeMutFromAttributes(chrom, start, end, ref_allele, alt_allele, build)
m1_annotated = tabixIndexedVcfDatasource.annotate_mutation(m1)
m1_annotation = m1_annotated.getAnnotation("ESP_AF")
cur_annotation = Annotation(value="", datasourceName="ESP", dataType="Float",
description="Allele Frequency", tags=[TagConstants.INFO, TagConstants.SPLIT],
number=-1)
self.assertTrue(m1_annotation.isEqual(cur_annotation), "Annotations do not match.")
m1_annotation = m1_annotated.getAnnotation("ESP_X")
cur_annotation = Annotation(value="", datasourceName="ESP", dataType="String",
description="A random variable, X", tags=[TagConstants.INFO, TagConstants.NOT_SPLIT],
number=2)
self.assertTrue(m1_annotation.isEqual(cur_annotation), "Annotations do not match.")
m1_annotation = m1_annotated.getAnnotation("ESP_H2")
cur_annotation = Annotation(value="", datasourceName="ESP", dataType="Flag",
description="HapMap2 membership", tags=[TagConstants.INFO, TagConstants.NOT_SPLIT],
number=0)
self.assertTrue(m1_annotation.isEqual(cur_annotation), "Annotations do not match.")
m1_annotation = m1_annotated.getAnnotation("ESP_Y")
cur_annotation = Annotation(value="", datasourceName="ESP", dataType="String",
description="A random variable, Y", tags=[TagConstants.INFO, TagConstants.NOT_SPLIT],
number=-2)
self.assertTrue(m1_annotation.isEqual(cur_annotation), "Annotations do not match.")
m1_annotation = m1_annotated.getAnnotation("ESP_Z")
cur_annotation = Annotation(value="", datasourceName="ESP", dataType="Float",
description="A random variable, Z", tags=[TagConstants.INFO,
TagConstants.NOT_SPLIT], number=3)
self.assertTrue(m1_annotation.isEqual(cur_annotation), "Annotations do not match.")
def testExampleVcfDBAnnotationWithIndelAvgMatch(self):
"""
"""
tabixIndexedVcfDirName = os.path.join(*["testdata", "vcf_db_avg", "hg19"])
tabixIndexedVcfDatasource = DatasourceFactory.createDatasource(
os.path.join(tabixIndexedVcfDirName, "vcf_db_avg.config"), tabixIndexedVcfDirName)
chrom = "4"
start = "1234567"
end = "1234567"
ref_allele = "GTC"
alt_allele = "GTCTTA"
build = "hg19"
m1 = MutUtils.initializeMutFromAttributes(chrom, start, end, ref_allele, alt_allele, build)
m1_annotated = tabixIndexedVcfDatasource.annotate_mutation(m1)
m1_annotation = m1_annotated.getAnnotation("ESP_AF")
cur_annotation = Annotation(value="0.5", datasourceName="ESP", dataType="Float",
description="Allele Frequency", tags=[TagConstants.INFO, TagConstants.SPLIT],
number=-1)
self.assertTrue(m1_annotation.isEqual(cur_annotation), "Annotations do not match.")
m1_annotation = m1_annotated.getAnnotation("ESP_AC")
cur_annotation = Annotation(value="3.0", datasourceName="ESP", dataType="Float",
description="Allele Count", tags=[TagConstants.INFO, TagConstants.NOT_SPLIT],
number=None)
self.assertTrue(m1_annotation.isEqual(cur_annotation), "Annotations do not match.")
m1_annotation = m1_annotated.getAnnotation("ESP_H2")
cur_annotation = Annotation(value="False|False|False", datasourceName="ESP", dataType="String",
description="HapMap2 membership", tags=[TagConstants.INFO, TagConstants.NOT_SPLIT],
number=None)
self.assertTrue(m1_annotation.isEqual(cur_annotation), "Annotations do not match.")
m1_annotation = m1_annotated.getAnnotation("ESP_AA")
cur_annotation = Annotation(value="T", datasourceName="ESP", dataType="String",
description="Ancestral Allele", tags=[TagConstants.INFO, TagConstants.NOT_SPLIT],
number=1)
self.assertTrue(m1_annotation.isEqual(cur_annotation), "Annotations do not match.")
m1_annotation = m1_annotated.getAnnotation("ESP_Z")
cur_annotation = Annotation(value="2.0,3.0,3.0", datasourceName="ESP", dataType="Float",
description="A random variable, Z", tags=[TagConstants.INFO,
TagConstants.NOT_SPLIT], number=3)
self.assertTrue(m1_annotation.isEqual(cur_annotation), "Annotations do not match.")
def test_convert_genomic_space_to_transcript_space(self):
base_config_location = "testdata/ensembl/saccer/"
ensembl_ds = DatasourceFactory.createDatasource(base_config_location + "ensembl.config", base_config_location)
tx = ensembl_ds.get_overlapping_transcripts("I", "350", "350") # transcript starts at 335.
start, end = TranscriptProviderUtils.convert_genomic_space_to_transcript_space("350", "350", tx[0])
self.assertTrue(start == end)
self.assertTrue(start == 16)
tx = ensembl_ds.get_overlapping_transcripts("II", "764690", "764690") # transcript starts at 764697 (strand is '-').
start, end = TranscriptProviderUtils.convert_genomic_space_to_transcript_space("764690", "764690", tx[0])
self.assertTrue(start == end)
self.assertTrue(start == 7)
start, end = TranscriptProviderUtils.convert_genomic_space_to_transcript_space("764680", "764690", tx[0])
self.assertTrue(start == (end - 10))
self.assertTrue(start == 7)
def testTCGAMAFAsInputAndQuickAnnotate(self):
""" Test that we can take in a TCGA MAF (using MAFLITE), do annotating, and still render it properly """
inputFilename = "testdata/maf/Patient0.maf.annotated"
tmp = MafliteInputMutationCreator(inputFilename,
'configs/maflite_input.config')
outputFilename = "out/testTCGAMAFAsInputAndQuickAnnotate.tsv"
outputRenderer = TcgaMafOutputRenderer(
outputFilename, 'configs/tcgaMAF2.4_output.config')
annotator = Annotator()
annotator.setInputCreator(tmp)
annotator.setOutputRenderer(outputRenderer)
ds = DatasourceFactory.createDatasource(
"testdata/thaga_janakari_gene_ds/hg19/tj_data.config",
"testdata/thaga_janakari_gene_ds/hg19/")
annotator.addDatasource(ds)
annotator.annotate()
statinfo = os.stat(outputFilename)
self.assertTrue(
statinfo.st_size > 0,
"Generated MAF file (" + outputFilename + ") is empty.")
tsvReaderIn = GenericTsvReader(inputFilename)
tsvReader = GenericTsvReader(outputFilename)
self.assertTrue(tsvReader.getComments().find('#version') != -1,
"First line did not specify a version number")
self.assertTrue("i_TJ_Data_Why" in tsvReader.getFieldNames(),
"New field missing (i_TJ_Data_Why) from header")
self.assertTrue("i_TJ_Data_Who" in tsvReader.getFieldNames(),
"New field missing (i_TJ_Data_Who) from header")
ctrOut = 0
for lineDict in tsvReader:
ctrOut += 1
ctrIn = 0
for lineDict in tsvReaderIn:
ctrIn += 1
ctrIn += len(tsvReaderIn.getCommentsAsList())
ctrOut += len(tsvReader.getCommentsAsList())
self.assertTrue(
ctrOut == (ctrIn + 2),
"Output file should have same number of lines plus two (for maf version and Oncotator version comments) as input file. (In,Out): "
+ str(ctrIn) + ", " + str(ctrOut))
def testDoubleAnnotationError(self):
''' Given a maf file that used to cause a duplicate annotation exception, do not throw that (or any) exception. '''
outputFilename = 'out/genericGenomePositionDoubleAnnotationTest.out.tsv'
gpDS = DatasourceFactory.createDatasource(
"testdata/small_genome_position_tsv_ds/oreganno_trim.config",
"testdata/small_genome_position_tsv_ds/")
annotator = Annotator()
annotator.setInputCreator(
MafliteInputMutationCreator(
'testdata/maflite/testDoubleAnnotate.maf.tsv'))
annotator.setOutputRenderer(SimpleOutputRenderer(outputFilename))
annotator.addDatasource(gpDS)
testFilename = annotator.annotate()
# Make sure that some values were populated
self.assertTrue(os.path.exists(testFilename))
def test_simple_genes_by_region_annotation(self):
"""Test web api backend call /genes/ """
# http://www.broadinstitute.org/oncotator/genes/chr22_22112223_22312558/
# Two genes: chr22:22,112,223-22,312,558
datasource_list = DatasourceFactory.createDatasources(self._determine_db_dir(), "hg19", isMulticore=False)
annotator = Annotator()
for ds in datasource_list:
annotator.addDatasource(ds)
# Here is what the API would call....
txs = annotator.retrieve_transcripts_by_region("22", 22112223, 22312558)
self.assertTranscriptsFound(txs)
mut_dict = annotator.annotate_genes_given_txs(txs)
# Each mut will be for a separate gene
for gene in mut_dict.keys():
mut = mut_dict[gene]
alt_accessions = mut['UniProt_alt_uniprot_accessions'].split("|")
tcgascape_amp_peaks = mut['TCGAScape_Amplification_Peaks'].split("|")
tcgascape_del_peaks = mut['TCGAScape_Deletion_Peaks'].split("|")
tumorscape_amp_peaks = mut['TUMORScape_Amplification_Peaks'].split("|")
tumorscape_del_peaks = mut['TUMORScape_Deletion_Peaks'].split("|")
full_name = mut['HGNC_Approved Name']
cosmic = {"tissue_types_affected": mut['COSMIC_Tissue_tissue_types_affected'], "total_alterations_in_gene": mut["COSMIC_Tissue_tissue_types_affected"]}
alt_aliases = list(itertools.chain([mut["HGNC_Previous Symbols"].split(", "), mut["HGNC_Synonyms"].split(", ")]))
location = mut["HGNC_Chromosome"]
uniprot_accession = mut["UniProt_uniprot_accession"]
transcripts = mut['transcripts']
self.assertTrue(transcripts is not None)
self.assertTrue(len(transcripts) > 0)
self.assertTrue(transcripts.startswith('ENST'))
strand = mut['strand']
klass = mut['class']
uniprot_experimentals = mut['UniProt_AA_experimental_info'].split("|")
self.assertTrue(uniprot_experimentals is not None)
uniprot_natural_variations = mut['UniProt_AA_natural_variation'].split("|")
uniprot_regions = mut['UniProt_AA_region'].split("|")
uniprot_sites = mut['UniProt_AA_site'].split("|")
uniprot_go_biological_processes = mut["UniProt_GO_Biological_Process"].split("|")
uniprot_go_cellular_components = mut["UniProt_GO_Cellular_Component"].split("|")
self.assertTrue(uniprot_go_cellular_components is not None)
uniprot_go_molecular_functions = mut["UniProt_GO_Molecular_Function"].split("|")
pass
def test_querying_transcripts_by_region(self):
"""Test web api backend call /transcripts/.... """
datasource_list = DatasourceFactory.createDatasources(
self._determine_db_dir(), "hg19", isMulticore=False)
annotator = Annotator()
for ds in datasource_list:
annotator.addDatasource(ds)
txs = annotator.retrieve_transcripts_by_region("4", 50164411, 60164411)
self.assertTranscriptsFound(txs)
## Here is an example of getting enough data to populate the json in doc/transcript_json_commented.json.txt
# None of these values are validated.
for tx in txs:
transcript_id = tx.get_transcript_id()
tx_start = tx.determine_transcript_start()
tx_end = tx.determine_transcript_stop()
gene = tx.get_gene()
chr = tx.get_contig()
n_exons = len(tx.get_exons())
strand = tx.get_strand()
footprint_start, footprint_end = tx.determine_cds_footprint()
klass = tx.get_gene_type()
cds_start = tx.determine_cds_start()
cds_end = tx.determine_cds_stop()
id = tx.get_gene_id()
genomic_coords = [[exon[0], exon[1]] for exon in tx.get_exons()]
transcript_coords = [[
TranscriptProviderUtils.convert_genomic_space_to_exon_space(
exon[0] + 1, exon[1], tx)
] for exon in tx.get_exons()]
code_len = int(cds_end) - int(cds_start) + 1
# If refseq datasources are not available, this will fail.
# Step 2 annotate the transcript, which produces a dummy mutation with the refseq annotations.
dummy_mut = annotator.annotate_transcript(tx)
refseq_mRNA_id = dummy_mut["gencode_xref_refseq_mRNA_id"]
refseq_prot_id = dummy_mut["gencode_xref_refseq_prot_acc"]
# Description is unavailable right now
description = ""
self.assertTrue(refseq_mRNA_id is not None)
self.assertTrue(refseq_prot_id is not None)
self.assertTrue(len(transcript_coords) == n_exons)
def testBasicCosmicInit(self):
""" Very simple test that will create a datasource from a sample datasource directory.
The directory conforms to the standard datasource structure, including placement of the config file.
"""
ds = DatasourceFactory.createDatasource(
'testdata/small_cosmic/small_cosmic.config',
"testdata/small_cosmic")
m = MutationDataFactory.default_create()
m.chr = 19
m.start = 58858921
m.end = 58858921
m = ds.annotate_mutation(m)
self.assertTrue(
m['COSMIC_overlapping_mutation_AAs'] == 'p.P426P(1)',
"Did not properly annotate mutation: " +
m['COSMIC_overlapping_mutation_AAs'])
