def _create_test_gencode_ds(base_output_filename, protein_id_mapping_file,
gencode_version):
genes = [
"MAPK1", "MUC16", "PIK3CA", "YPEL1", "KRTAP4-7", "MAT2A",
"DDX11L10"
]
gtf_list = []
fasta_list = []
for gene in genes:
gtf_list.append("testdata/gencode/" + gene + ".gencode.v" +
str(gencode_version) + ".annotation.gtf")
fasta_list.append("testdata/gencode/" + gene + ".gencode.v" +
str(gencode_version) + ".pc_transcripts.fa")
shutil.rmtree(base_output_filename + ".transcript.idx",
ignore_errors=True)
shutil.rmtree(base_output_filename + ".transcript_by_gene.idx",
ignore_errors=True)
shutil.rmtree(base_output_filename + ".transcript_by_gp_bin.idx",
ignore_errors=True)
genome_build_factory = GenomeBuildFactory()
genome_build_factory.construct_ensembl_indices(
gtf_list,
fasta_list,
base_output_filename,
protein_id_mapping_file=protein_id_mapping_file)
ensembl_ds = EnsemblTranscriptDatasource(base_output_filename,
title="GENCODE",
version="v" +
str(gencode_version),
tx_filter="basic")
return ensembl_ds
def createTranscriptProviderDatasource(config,
tx_mode="CANONICAL",
protocol="file"):
""" Creates a GENCODE or Gaf 3.0 datasource from a config file. Determines which is available automatically,
For GAF 3.0, assumes a gaf3.0 section with keys: gaf_fname and gaf_transcript_seqs_fname
"""
if os.path.exists(config.get("gencode", "gencodeDir")):
gencode_dir = config.get("gencode", "gencodeDir")
result_ds = EnsemblTranscriptDatasource(
gencode_dir + "/gencode.v19.annotation.gtf",
title="GENCODE",
version="TEST v19",
tx_filter="basic",
tx_mode=tx_mode)
else:
try:
gaf_fname = config.get("gaf3.0", "gaf_fname")
gaf_transcripts_fname = config.get(
"gaf3.0", "gaf_transcript_seqs_fname")
result_ds = Gaf(gaf_fname,
gaf_transcripts_fname,
tx_mode=tx_mode,
protocol=protocol)
except Exception as gaf_failure_reason:
raise Exception(
"Couldn't create a transcript provider datasource, no gencode dir found and %s"
% gaf_failure_reason)
return result_ds
def _create_ensembl_ds_from_saccer(self):
gencode_input_gtf = "testdata/Saccharomyces_cerevisiae.EF4.71_trim.gtf"
gencode_input_fasta = "testdata/Saccharomyces_cerevisiae.EF4.71_trim.cdna.all.fa"
base_output_filename = "out/test_saccer_ds"
shutil.rmtree(base_output_filename + ".transcript.idx", ignore_errors=True)
shutil.rmtree(base_output_filename + ".transcript_by_gene.idx", ignore_errors=True)
shutil.rmtree(base_output_filename + ".transcript_by_gp_bin.idx", ignore_errors=True)
genome_build_factory = GenomeBuildFactory()
genome_build_factory.construct_ensembl_indices([gencode_input_gtf], [gencode_input_fasta], base_output_filename)
ensembl_ds = EnsemblTranscriptDatasource(base_output_filename, title="ensembl", version="71")
return ensembl_ds
def test_intitialize(self):
"""Test a simple initialization of an ensembl datasource """
base_config_location = "testdata/ensembl/saccer/"
config_parser = ConfigUtils.createConfigParser(base_config_location + "ensembl.config")
title = config_parser.get("general", "title")
version = config_parser.get("general", "version")
src_file = config_parser.get("general", "src_file")
ensembl_ds = EnsemblTranscriptDatasource(title=title, version=version, src_file=src_file)
self.assertIsNotNone(ensembl_ds)
ensembl_ds.set_tx_mode(TranscriptProvider.TX_MODE_BEST_EFFECT)
self.assertTrue(TranscriptProvider.TX_MODE_BEST_EFFECT == ensembl_ds.get_tx_mode())
def test_simple_annotate(self):
""" Annotate a simple example.
"""
base_config_location = "testdata/ensembl/saccer/"
config_parser = ConfigUtils.createConfigParser(base_config_location + "ensembl.config")
title = config_parser.get("general", "title")
version = config_parser.get("general", "version")
src_file = config_parser.get("general", "src_file")
ensembl_ds = EnsemblTranscriptDatasource(title=title, version=version, src_file=src_file)
m = MutationData()
m.chr = "22"
m.start = "22161963"
m.end = "22161963"
m.ref_allele = "C"
m.alt_allele = "A"
m2 = ensembl_ds.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
