def testExtentOutOfRangeError(self):
''' If a window is specified that extends beyond the beginning or end of a file, truncate the ref_context.
Use what is left for gc_content as well.'''
ds = ReferenceDatasource('testdata/reference_ds',
windowSizeRef=6,
windowSizeGCContent=5)
m = MutationDataFactory.default_create()
m.chr = "22"
m.start = "4"
m.end = "4"
# "CCCAAGCTAAACCCAGGCCAC"
groundTruth = "CCCAAGCTAA"
guess = ds.annotate_mutation(m)
self.assertTrue(
guess['ref_context'] == groundTruth,
"ref_context was not populated properly: " +
str(guess['ref_context']))
# gc_content is rounded to 3 decimal places
self.assertTrue(
fabs(float(guess['gc_content']) - (float(5) / float(9))) < .001,
"gc_content was not populated properly: " +
str(guess['gc_content']))
def testEmptyAnswer(self):
''' The Reference Datasource should return a blank result if the chromosome is not found.
Note: A log entry should also be written, but this is not tested. '''
self.logger.info("Please ignore the next logging warning: testdata/reference_ds/chrTHIS_DOES_NOT_EXIST.txt not found. Please add it.")
ds = ReferenceDatasource('testdata/reference_ds')
m = MutationData()
m.chr = "THIS_DOES_NOT_EXIST"
m.start = "11"
m.end = "11"
groundTruth = ""
# remember that the annotate_mutation returns a generator, so we use an iterator
guess = ds.annotate_mutation(m)
self.assertTrue(guess['ref_context'] == groundTruth, "ref_context was not populated properly -- should be blank: " + str(guess['ref_context']))
def testFilenameDetermination(self):
''' Test that proper conversions are being done for chromosome to flat filename '''
ds = ReferenceDatasource('testdata/reference_ds')
self.assertTrue(
ds.convertMutationChrToFilename("GL000211.1") ==
'chrUn_gl000211.txt', "Did not find GL file: " +
str(ds.convertMutationChrToFilename("GL000211.1")))
self.assertTrue(
ds.convertMutationChrToFilename("X") == 'chrX.txt',
"Did not find chrX file: " +
str(ds.convertMutationChrToFilename("X")))
self.assertTrue(
ds.convertMutationChrToFilename("GL000209.1") ==
'chr19_gl000209_random.txt', "Did not find GL chr19 file: " +
str(ds.convertMutationChrToFilename("GL000209.1")))
def testSimpleGLAnnotate(self):
''' Test a simple annotation case. Make sure that the ref_context and gc_content annotations are correct. '''
ds = ReferenceDatasource('testdata/reference_ds', windowSizeGCContent=5)
m = MutationData()
m.chr = "GL000211.1"
m.start = "11"
m.end = "11"
groundTruth = "gaattctttttcaagtaagtc"
guess = ds.annotate_mutation(m)
self.assertTrue(guess['ref_context'] == groundTruth, "ref_context was not populated properly: " + str(m['ref_context']))
# gc_content is rounded to 3 decimal places
self.assertTrue(fabs(float(guess['gc_content']) - (float(3)/float(11))) < .001, "gc_content was not populated properly: " + str(m['gc_content']))
def testSimpleAnnotate(self):
''' Perform a simple test of one of the aligned chromosomes (chr22) and make sure that we get a reasonable answer.
'''
ds = ReferenceDatasource('testdata/reference_ds', windowSizeGCContent=5)
m = MutationData()
m.chr = "22"
m.start = "11"
m.end = "11"
groundTruth = "CCCAAGCTAAACCCAGGCCAC"
guess = ds.annotate_mutation(m)
self.assertTrue(guess['ref_context'] == groundTruth, "ref_context was not populated properly: " + str(guess['ref_context']))
# gc_content is rounded to 3 decimal places
self.assertTrue(fabs(float(guess['gc_content'])- (float(6)/float(11))) < .001, "gc_content was not populated properly: " + str(guess['gc_content']))
def createReferenceDatasource(config):
refFilename = config.get("ref_hg", "refDir")
return ReferenceDatasource(refFilename)
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