def testRangeAnnotation(self): ''' Test a simple case with range. ''' datasource = GenericGeneProteinPositionDatasource("testdata/simple_uniprot_natvar/simple_uniprot_natvar.tsv", title="UniProt_NatVar", version="2011_09") m = MutationData() m.createAnnotation("gene", "TP53") m.createAnnotation("protein_change", "p.SLEELEE370_376del") # This is not valid, but does the test. m2 = datasource.annotate_mutation(m) annotationName= "UniProt_NatVar_natural_variations" self.assertTrue(sorted(m[annotationName].split("|")) == sorted("K -> Q (in a sporadic cancer; somatic mutation).|S -> T (in a sporadic cancer; somatic mutation).|S -> A (in a sporadic cancer; somatic mutation).".split("|")), "Incorrect annotation value seen: " + m[annotationName])
def testBasicAnnotation(self): ''' Test an extremely simple case. ''' datasource = GenericGeneProteinPositionDatasource("testdata/simple_uniprot_natvar/simple_uniprot_natvar.tsv", title="UniProt_NatVar", version="2011_09") m = MutationData() m.createAnnotation("gene", "TP53") m.createAnnotation("protein_change", "p.S376C") m2 = datasource.annotate_mutation(m) annotationName= "UniProt_NatVar_natural_variations" self.assertTrue(sorted(m[annotationName].split("|")) == sorted("S -> T (in a sporadic cancer; somatic mutation).|S -> A (in a sporadic cancer; somatic mutation).".split("|")), "Incorrect annotation value seen: " + m[annotationName])
def testRangeAnnotation(self): ''' Test a simple case with range. ''' datasource = GenericGeneProteinPositionDatasource("testdata/simple_uniprot_natvar/simple_uniprot_natvar.tsv", title="UniProt_NatVar", version="2011_09") m = MutationDataFactory.default_create() m.createAnnotation("gene", "TP53") m.createAnnotation("protein_change", "p.SLEELEE370_376del") # This is not valid, but does the test. m2 = datasource.annotate_mutation(m) annotationName= "UniProt_NatVar_natural_variations" self.assertTrue(sorted(m[annotationName].split("|")) == sorted("K -> Q (in a sporadic cancer; somatic mutation).|S -> T (in a sporadic cancer; somatic mutation).|S -> A (in a sporadic cancer; somatic mutation).".split("|")), "Incorrect annotation value seen: " + m[annotationName])
def testBasicAnnotation(self): ''' Test an extremely simple case. ''' datasource = GenericGeneProteinPositionDatasource("testdata/simple_uniprot_natvar/simple_uniprot_natvar.tsv", title="UniProt_NatVar", version="2011_09") m = MutationData() m.createAnnotation("gene", "TP53") m.createAnnotation("protein_change", "p.S376C") m.createAnnotation("other_transcripts", "TP53_uc002gig.1_Intron|TP53_uc002gih.2_Intron|TP53_uc010cne.1_RNA|TP53_uc010cnf.1_3'UTR|TP53_uc010cng.1_3'UTR|TP53_uc002gii.1_Missense_Mutation_p.S244C|TP53_uc010cnh.1_3'UTR|TP53_uc010cni.1_3'UTR|TP53_uc002gij.2_Missense_Mutation_p.S376C") m2 = datasource.annotate_mutation(m) annotationName= "UniProt_NatVar_natural_variations" self.assertTrue(sorted(m[annotationName].split("|")) == sorted("S -> T (in a sporadic cancer; somatic mutation).|S -> A (in a sporadic cancer; somatic mutation).".split("|")), "Incorrect annotation value seen: " + m[annotationName])
def testMissingAnnotations(self): ''' Tests that if the required annotations ("gene", "protein_change", and "other_transcripts") are missing, an exception is thrown. ''' datasource = GenericGeneProteinPositionDatasource("testdata/simple_uniprot_natvar/simple_uniprot_natvar.tsv", title="SmallNatVar", version="test") m = MutationData() m.createAnnotation("gene", "TP53") #m.createAnnotation("protein_change", "p.S376C") self.assertRaisesRegexp(MissingAnnotationException, "protein_change", datasource.annotate_mutation, m)
def createDatasourceFromConfigParser(configParser, leafDir): """ configParser -- config parser instance from the config file in the leafdir. For information on config file format/conventions see (TODO) leafDir -- contains the file and necessary files (post indexing and install steps) to instantiate a datasource. """ result = None # Determine the type dsType = configParser.get("general", "type") # TODO: Replace these if statements with something a bit more robust, such as a proper dependency injection framework filePrefix = leafDir + "/" if dsType == "gaf": gaf_fname = filePrefix + configParser.get('general', 'gaf_fname') gaf_transcript_sequences_fname = filePrefix + configParser.get('general', 'gaf_transcript_seqs_fname') result = Gaf(gaf_fname, gaf_transcript_sequences_fname, title=configParser.get("general", "title"), version=configParser.get("general", "version"), protocol=configParser.get("general", "protocol")) elif dsType == "dbsnp": result = dbSNP(filePrefix + configParser.get('general', 'src_file'), title=configParser.get('general', 'title'), version=configParser.get('general', 'version')) elif dsType == "ensembl": result = EnsemblTranscriptDatasource(filePrefix + configParser.get('general', 'src_file'), title=configParser.get('general', 'title'), version=configParser.get('general', 'version'), tx_filter=configParser.get('general', 'transcript_filter')) elif dsType == "cosmic": result = Cosmic(src_file=filePrefix + configParser.get('general', 'src_file'), version=configParser.get('general', 'version'), gpp_tabix_file=filePrefix + configParser.get('general', 'gpp_src_file')) elif dsType == 'ref': if configParser.has_option('general', 'windowSizeRef'): window_size = configParser.get('general', 'windowSizeRef') else: window_size = 10 result = ReferenceDatasource(filePrefix, title=configParser.get("general", "title"), version=configParser.get('general', 'version'), windowSizeRef=window_size) elif dsType == 'gene_tsv': result = GenericGeneDatasource(src_file=filePrefix + configParser.get('general', 'src_file'), title=configParser.get("general", "title"), version=configParser.get('general', 'version'), geneColumnName=configParser.get('general', 'gene_col')) elif dsType == 'transcript_tsv': result = GenericTranscriptDatasource(src_file=filePrefix + configParser.get('general', 'src_file'), title=configParser.get("general", "title"), version=configParser.get('general', 'version'), geneColumnName=configParser.get('general', 'transcript_col')) elif dsType == 'vc_tsv': result = GenericVariantClassificationDatasource(src_file=filePrefix + configParser.get('general', 'src_file'), title=configParser.get("general", "title"), version=configParser.get('general', 'version'), geneColumnName=configParser.get('general', 'vc_col')) elif dsType == 'gp_tsv': result = GenericGenomicPositionDatasource(src_file=filePrefix + configParser.get('general', 'src_file'), title=configParser.get("general", "title"), version=configParser.get('general', 'version'), gpColumnNames=configParser.get('general', 'genomic_position_cols')) elif dsType == 'gm_tsv': result = GenericGenomicMutationDatasource(src_file=filePrefix + configParser.get('general', 'src_file'), title=configParser.get("general", "title"), version=configParser.get('general', 'version'), gpColumnNames=configParser.get('general', 'genomic_position_cols')) elif dsType == 'gm_tsv_reverse_complement': result = GenericGenomicMutationDatasource(src_file=filePrefix + configParser.get('general', 'src_file'), title=configParser.get("general", "title"), version=configParser.get('general', 'version'), gpColumnNames=configParser.get('general', 'genomic_position_cols'), use_complementary_strand_alleles_for_negative_strand_transcripts=True) elif dsType == 'gpp_tsv': result = GenericGeneProteinPositionDatasource(src_file=filePrefix + configParser.get('general', 'src_file'),title=configParser.get("general", "title"), version=configParser.get('general', 'version'), gpColumnNames=configParser.get('general', 'gene_protein_position_cols')) elif dsType == "transcript_to_uniprot_aa": result = TranscriptToUniProtProteinPositionTransformingDatasource(title=configParser.get("general", "title"), version=configParser.get('general', 'version'), src_file="file://" + filePrefix + configParser.get('general', 'src_file'), # three slashes for sqlite inputPositionAnnotationName=configParser.get('general', 'inputPositionAnnotationName'), outputPositionAnnotationName=configParser.get('general','outputPositionAnnotationName')) elif dsType == "mock_exception": result = MockExceptionThrowingDatasource(title=configParser.get("general", "title"), version=configParser.get('general', 'version')) elif dsType == "indexed_vcf": result = IndexedVcfDatasource(src_file=filePrefix + configParser.get('general', 'src_file'), title=configParser.get("general", "title"), version=configParser.get('general', 'version'), match_mode=configParser.get('general', 'match_mode')) elif dsType == "indexed_tsv": columnNames = configParser.get("general", "column_names") columnNames = columnNames.split(",") annotationColumnNames = configParser.get("general", "annotation_column_names") annotationColumnNames = annotationColumnNames.split(",") indexColumnNames = configParser.get("general", "index_column_names") indexColumnNames = indexColumnNames.split(",") DatasourceFactory._log_missing_column_name_msg(columnNames, annotationColumnNames) columnDataTypes = dict() for columnName in annotationColumnNames: if columnName.strip() == "": continue columnDataTypes[columnName] = configParser.get("data_types", columnName) result = IndexedTsvDatasource(src_file=filePrefix + configParser.get("general", "src_file"), title=configParser.get("general", "title"), version=configParser.get("general", "version"), colNames=columnNames, annotationColNames=annotationColumnNames, indexColNames=indexColumnNames, match_mode=configParser.get("general", "match_mode"), colDataTypes=columnDataTypes) elif dsType == 'bigwig': if not NGSLIB_INSTALLED: raise RuntimeError("Bigwig datasource found in db-dir but ngslib library not installed.") result = BigWigDatasource(src_file=filePrefix + configParser.get('general', 'src_file'), title=configParser.get("general", "title"), version=configParser.get('general', 'version')) else: raise RuntimeError('Unknown datasource type: %s' % dsType) hashcode = DatasourceFactory._retrieve_hash_code(leafDir) result.set_hashcode(hashcode) return result