def createDatasource(tmpDir):
# Parse the input arguments.
"""
:param tmpDir: temporary directory
"""
args = parseOptions()
validateArgs(args)
index_columns = args.index_columns
ds_name = args.name
ds_version = args.version
ds_type = args.ds_type
ds_foldername = args.ds_foldername
dbDir = args.dbDir
genome_build = args.genome_build
ds_file = args.ds_file
ds_match_mode = args.match_mode
# Parameters for indexed_tsv only.
ds_annotation_columns = args.annotation_columns
# Create appropriate subdirectory in tmp dir.
destDir = os.path.join(*[tmpDir, ds_foldername, genome_build])
os.makedirs(destDir)
# Create a basic logger to a file
loggingFormat = '%(asctime)s %(levelname)s [%(name)s:%(lineno)d] %(message)s'
logging.basicConfig(filename="initializeDatasource.log",
level=logging.INFO,
format=loggingFormat)
# Add a console logger to the root logger, which means that all loggers generated will have the console dump.
# Output on the console will be the same as what is in the log file.
ch = logging.StreamHandler()
ch.setLevel(logging.INFO)
formatter = logging.Formatter(loggingFormat)
ch.setFormatter(formatter)
logging.getLogger('').addHandler(ch)
# Copy the tsv file into genome build dir
DatasourceInstallUtils.create_datasource(destDir, ds_file, ds_foldername,
ds_name, ds_type, ds_version,
index_columns,
ds_annotation_columns,
ds_match_mode)
logging.getLogger(__name__).info("Config file created: " +
os.path.join(destDir, ds_foldername) +
".config")
# Last step: Copy the directory to the destination dbDir.
shutil.copytree(symlinks=True,
src=os.path.join(tmpDir, ds_foldername),
dst=os.path.join(dbDir, ds_foldername))
logging.getLogger(
__name__).info("Datasource copied from temp location to " +
os.path.join(dbDir, ds_foldername))
def testCreateGPTsvDatasource(self):
"""
"""
datasourceFilename = "testdata/small_genome_position_tsv_ds/oreganno_trim.hg19.txt"
datasourceType = "gp_tsv"
datasourceName = "ORegAnno"
datasourceFoldername = "ORegAnno"
datasourceVersion = "UCSC Track"
genomeBuild = "hg19"
genomicPositionColumnNames = "hg19.oreganno.chrom,hg19.oreganno.chromStart,hg19.oreganno.chromEnd"
tmpDir = tempfile.mkdtemp()
destDir = os.path.join(*[tmpDir, datasourceFoldername, genomeBuild])
os.makedirs(destDir)
DatasourceInstallUtils.create_datasource(destDir, datasourceFilename, datasourceFoldername, datasourceName,
datasourceType, datasourceVersion, genomicPositionColumnNames)
datasourceFilename = "oreganno_trim.hg19.txt"
configFilename = os.path.join(*[destDir, "ORegAnno.config"])
configParser = ConfigUtils.createConfigParser(configFilename)
self.assertTrue(configParser.has_section("general"), "general section is missing.")
self.assertTrue(configParser.has_option("general", "type"), "type option is missing in general section.")
self.assertTrue(configParser.has_option("general", "src_file"),
"src_file option is missing in general section.")
self.assertTrue(configParser.has_option("general", "title"), "title option is missing in general section.")
self.assertTrue(configParser.has_option("general", "version"), "version option is missing in general section.")
self.assertTrue(configParser.has_option("general", "genomic_position_cols"),
"genomic_position_cols option is missing in general section.")
self.assertEqual(configParser.get("general", "type"), datasourceType,
"Expected data source type is %s but was %s."
% (datasourceType, configParser.get("general", "type")))
self.assertEqual(configParser.get("general", "src_file"), datasourceFilename,
"Expected data source src_file is %s but was %s."
% (datasourceFilename, configParser.get("general", "src_file")))
self.assertEqual(configParser.get("general", "title"), datasourceName,
"Expected data source title is %s but was %s."
% (datasourceName, configParser.get("general", "title")))
self.assertEqual(configParser.get("general", "version"), datasourceVersion,
"Expected data source version is %s but was %s."
% (datasourceVersion, configParser.get("general", "version")))
self.assertEqual(configParser.get("general", "genomic_position_cols"), genomicPositionColumnNames,
"Expected data source genomic_position_cols is %s but was %s."
% (genomicPositionColumnNames, configParser.get("general", "genomic_position_cols")))
self.assertTrue(os.path.exists(os.path.join(*[tmpDir, datasourceFoldername, genomeBuild + ".md5"])),
"No md5 file was generated.")
MutUtils.removeDir(tmpDir)
def testCreateIndexedVcfDatasource(self):
datasourceFilename = "testdata/vcf/example.vcf"
datasourceFoldername = "1000Genomes"
datasourceName = "1000Genomes"
datasourceType = "indexed_vcf"
datasourceVersion = "V4.1"
genomeBuild = "hg19"
tmpDir = tempfile.mkdtemp()
destDir = os.path.join(*[tmpDir, datasourceFoldername, genomeBuild])
os.makedirs(destDir)
DatasourceInstallUtils.create_datasource(destDir, datasourceFilename, datasourceFoldername, datasourceName,
datasourceType, datasourceVersion)
datasourceFilename = "example.tabix_indexed.vcf.gz"
configFilename = os.path.join(*[destDir, "1000Genomes.config"])
configParser = ConfigUtils.createConfigParser(configFilename)
self.assertTrue(configParser.has_section("general"), "general section is missing.")
self.assertTrue(configParser.has_option("general", "type"), "type option is missing in general section.")
self.assertTrue(configParser.has_option("general", "src_file"),
"src_file option is missing in general section.")
self.assertTrue(configParser.has_option("general", "title"), "title option is missing in general section.")
self.assertTrue(configParser.has_option("general", "version"), "version option is missing in general section.")
self.assertEqual(configParser.get("general", "type"), datasourceType,
"Expected data source type is %s but was %s."
% (datasourceType, configParser.get("general", "type")))
self.assertEqual(configParser.get("general", "src_file"), datasourceFilename,
"Expected data source src_file is %s but was %s."
% (datasourceFilename, configParser.get("general", "src_file")))
self.assertEqual(configParser.get("general", "title"), datasourceName,
"Expected data source title is %s but was %s."
% (datasourceName, configParser.get("general", "title")))
self.assertEqual(configParser.get("general", "version"), datasourceVersion,
"Expected data source version is %s but was %s."
% (datasourceVersion, configParser.get("general", "version")))
self.assertTrue(os.path.exists(os.path.join(*[tmpDir, datasourceFoldername, genomeBuild + ".md5"])),
"No md5 file was generated.")
# Data source was created correctly
tabixIndexedFilename = os.path.join(*[destDir, "example.tabix_indexed.vcf.gz"])
self.assertTrue(os.path.exists(tabixIndexedFilename), "No index file was generated.")
vcfReader = vcf.Reader(filename=tabixIndexedFilename, compressed=True, strict_whitespace=True)
vcfRecords = vcfReader.fetch(chrom=20, start=1230237, end=1230237)
for vcfRecord in vcfRecords:
self.assertEqual(vcfRecord.INFO["NS"], 3, "Expected %s but got %s." % (3, vcfRecord.INFO["NS"]))
self.assertEqual(vcfRecord.INFO["DP"], 13, "Expected %s but got %s." % (13, vcfRecord.INFO["DP"]))
MutUtils.removeDir(tmpDir)
def createDatasource(tmpDir):
# Parse the input arguments.
"""
:param tmpDir: temporary directory
"""
args = parseOptions()
validateArgs(args)
index_columns = args.index_columns
ds_name = args.name
ds_version = args.version
ds_type = args.ds_type
ds_foldername = args.ds_foldername
dbDir = args.dbDir
genome_build = args.genome_build
ds_file = args.ds_file
ds_match_mode = args.match_mode
# Parameters for indexed_tsv only.
ds_annotation_columns = args.annotation_columns
# Create appropriate subdirectory in tmp dir.
destDir = os.path.join(*[tmpDir, ds_foldername, genome_build])
os.makedirs(destDir)
# Create a basic logger to a file
loggingFormat = '%(asctime)s %(levelname)s [%(name)s:%(lineno)d] %(message)s'
logging.basicConfig(filename="initializeDatasource.log", level=logging.INFO, format=loggingFormat)
# Add a console logger to the root logger, which means that all loggers generated will have the console dump.
# Output on the console will be the same as what is in the log file.
ch = logging.StreamHandler()
ch.setLevel(logging.INFO)
formatter = logging.Formatter(loggingFormat)
ch.setFormatter(formatter)
logging.getLogger('').addHandler(ch)
# Copy the tsv file into genome build dir
DatasourceInstallUtils.create_datasource(destDir, ds_file, ds_foldername, ds_name, ds_type, ds_version,
index_columns, ds_annotation_columns, ds_match_mode)
logging.getLogger(__name__).info("Config file created: " + os.path.join(destDir, ds_foldername) + ".config")
# Last step: Copy the directory to the destination dbDir.
shutil.copytree(symlinks=True, src=os.path.join(tmpDir, ds_foldername), dst=os.path.join(dbDir, ds_foldername))
logging.getLogger(__name__).info("Datasource copied from temp location to " + os.path.join(dbDir, ds_foldername))
def testCreateIndexedTsvDatasource(self):
datasourceFilename = "testdata/ESP6500SI-V2.chr1.snps_indels.head.25.txt"
datasourceFoldername = "1000Genomes"
datasourceName = "1000Genomes"
datasourceType = "indexed_tsv"
datasourceVersion = "V4.1"
genomeBuild = "hg19"
indexColumnNames = "CHROM,POS,POS"
columnNames = "CHROM,POS,REF,ALT,DBSNP,EA_AC,AA_AC,TAC,MAF,GTS,EA_GTC,AA_GTC,GTC,DP,FG,GM,AA,AAC,PP,CDP,PH,CP,CG,GL,GS,CA,EXOME_CHIP,GWAS_PUBMED"
annotationColumnNames = "DBSNP,EA_AC,AA_AC,TAC"
tmpDir = tempfile.mkdtemp()
destDir = os.path.join(*[tmpDir, datasourceFoldername, genomeBuild])
os.makedirs(destDir)
DatasourceInstallUtils.create_datasource(destDir=destDir, ds_file=datasourceFilename,
ds_foldername=datasourceFoldername, ds_name=datasourceName,
ds_type=datasourceType, ds_version=datasourceVersion,
index_columns=indexColumnNames,
ds_annotation_columns=annotationColumnNames)
datasourceFilename = "ESP6500SI-V2.chr1.snps_indels.head.25.tabix_indexed.txt.gz"
configFilename = os.path.join(*[destDir, "1000Genomes.config"])
configParser = ConfigUtils.createConfigParser(configFilename)
self.assertTrue(configParser.has_section("general"), "general section is missing.")
self.assertTrue(configParser.has_option("general", "type"), "type option is missing in general section.")
self.assertTrue(configParser.has_option("general", "src_file"),
"src_file option is missing in general section.")
self.assertTrue(configParser.has_option("general", "title"), "title option is missing in general section.")
self.assertTrue(configParser.has_option("general", "version"), "version option is missing in general section.")
self.assertTrue(configParser.has_option("general", "column_names"),
"column_names option is missing in general section.")
self.assertTrue(configParser.has_option("general", "annotation_column_names"),
"annotation_column_names option is missing in general section.")
self.assertEqual(configParser.get("general", "type"), datasourceType,
"Expected data source type is %s but was %s."
% (datasourceType, configParser.get("general", "type")))
self.assertEqual(configParser.get("general", "src_file"), datasourceFilename,
"Expected data source src_file is %s but was %s."
% (datasourceFilename, configParser.get("general", "src_file")))
self.assertEqual(configParser.get("general", "title"), datasourceName,
"Expected data source title is %s but was %s."
% (datasourceName, configParser.get("general", "title")))
self.assertEqual(configParser.get("general", "version"), datasourceVersion,
"Expected data source version is %s but was %s."
% (datasourceVersion, configParser.get("general", "version")))
self.assertEqual(configParser.get("general", "column_names"), columnNames,
"Expected data source column names is %s but was %s."
% (columnNames, configParser.get("general", "column_names")))
self.assertEqual(configParser.get("general", "annotation_column_names"), annotationColumnNames,
"Expected data source annotation column names is %s but was %s."
% (annotationColumnNames, configParser.get("general", "annotation_column_names")))
self.assertTrue(os.path.exists(os.path.join(*[tmpDir, datasourceFoldername, genomeBuild + ".md5"])),
"No md5 file was generated.")
datasource = DatasourceFactory.createDatasource(configFilename, destDir)
m1 = MutationDataFactory.default_create()
m1.chr = "1"
m1.start = "802177"
m1.end = "802177"
m1.ref_allele = "T"
m1.alt_allele = "C"
m1_annotated = datasource.annotate_mutation(m1)
m1_annotation = m1_annotated.getAnnotation("1000Genomes_AA_AC")
cur_annotation = Annotation(value="2,866", datasourceName="1000Genomes", dataType="String",
description="",
tags=[TagConstants.INFO, TagConstants.NOT_SPLIT], number=None)
self.assertTrue(m1_annotation.isEqual(cur_annotation), "Annotations do not match.")
annotationNames = ["1000Genomes_CHROM", "1000Genomes_POS", "1000Genomes_REF", "1000Genomes_ALT",
"1000Genomes_GWAS_PUBMED"]
for annotationName in annotationNames:
self.assertTrue(annotationName not in m1_annotated, "m1_annotated was annotated with %s." % annotationName)
annotationNames = ["1000Genomes_DBSNP", "1000Genomes_EA_AC", "1000Genomes_AA_AC", "1000Genomes_TAC"]
for annotationName in annotationNames:
self.assertTrue(annotationName in m1_annotated, "m1_annotated was not annotated with %s value."
% annotationName)
MutUtils.removeDir(tmpDir)
