class BinIndex(object):
''' class to fetch and map locations to index bins
creates its own DB handle
b/c variants are usually incremental; stores current bin
and checks if variant is in that; if not fetches bin from DB
'''
def __init__(self, gusConfigFile=None, verbose=True):
self._gusConfigFile = gusConfigFile
self._verbose = verbose
self._currentBin = {}
self.__get_db_handle()
self._cursor = self._database.cursor("RealDictCursor")
def __get_db_handle(self):
''' create database connection '''
self._database = Database(self._gusConfigFile)
self._database.connect()
def close(self):
''' close db connection '''
self._cursor.close()
self._database.close()
def _update_current_bin_index(self, chrm, start, end):
''' query against database to get minimum enclosing bin;
set as new current bin'''
if self._verbose: warning("Updating current bin")
result = None
self._cursor.execute(BIN_INDEX_SQL, (chrm, start, end))
try:
self._currentBin = self._cursor.fetchone()
except ProgrammingError:
raise ProgrammingError('Could not map ' + chrm + ':' + xstr(start) + '-' + xstr(end) + ' to a bin.')
if self._verbose: warning(self._currentBin)
return result
def find_bin_index(self, chrm, start, end=None):
''' finds the bin index for the position;
if end == None assume SNV, and set to start'''
if end is None: end = start
if 'chr' not in chrm: chrm = 'chr' + xstr(chrm)
if bool(self._currentBin): # if a current bin exists and the variant falls in it, return it
if self._currentBin['bin_level'] >= 27: # otherwise may be a broad bin b/c of a indel; so need to do a lookup
brange = self._currentBin['location']
if self._currentBin['chromosome'] == chrm \
and start in brange and end in brange:
return self._currentBin['global_bin_path']
# otherwise, find & return the new bin
self._update_current_bin_index(chrm, start, end) # not in current bin, so update bin
return self._currentBin['global_bin_path']
class AlgorithmInvocation(object):
''' transaction management for algorithm invocation '''
def __init__(self,
script=None,
parameters=None,
commit=False,
gusConfigFile=None):
self._database = None
self._algorithm_invocation_id = None
self.__get_db_handle(gusConfigFile)
if script is not None:
self.insertAlgorithmInvocation(script, parameters, commit)
def __get_db_handle(self, gusConfigFile):
''' create database connection '''
self._database = Database(gusConfigFile)
self._database.connect()
def insertAlgorithmInvocation(self, script, parameters, commit):
''' create the entry for the algorithm invocation '''
sql = """INSERT INTO AlgorithmInvocation
(script_name, script_parameters, commit_mode) VALUES (%s, %s, %s)
RETURNING algorithm_invocation_id"""
with self._database.cursor() as cursor:
cursor.execute(sql, (script, parameters, commit))
self._algorithm_invocation_id = cursor.fetchone()[0]
self._database.commit()
def getAlgorithmInvocationId(self):
''' return algorithm invocation id '''
return self._algorithm_invocation_id
def close(self):
''' close db connection '''
self._database.close()
def load_annotation(chromosome):
''' parse over a JSON file, extract position, frequencies,
ids, and ADSP-ranked most severe consequence; bulk load using COPY '''
lfn = xstr(chromosome) + '.log'
lfh = open(lfn, 'w')
algInvocation = AlgorithmInvocation('parallel_load_dbsnp_vep_result.py',
json.dumps({'chromosome': chromosome}),
args.commit)
algInvocId = xstr(algInvocation.getAlgorithmInvocationId())
algInvocation.close()
warning("Algorithm Invocation ID", algInvocId, file=lfh, flush=True)
vepParser = VepJsonParser(args.rankingFile, verbose=True)
indexer = BinIndex(args.gusConfigFile, verbose=False)
database = Database(args.gusConfigFile)
database.connect()
fname = 'chr' + xstr(chromosome) + '.json.gz'
fname = path.join(args.dir, fname)
lineCount = 0
variantCount = 0
skipCount = 0
resume = True if args.resumeAfter is None else False
if not resume:
warning("--resumeAfter flag specified; Finding skip until point",
args.resumeAfter,
file=lfh,
flush=True)
previousSnp = None
with database.cursor() as cursor:
copyObj = io.StringIO()
with open(fname, 'r') as fhandle:
mappedFile = mmap.mmap(fhandle.fileno(), 0,
prot=mmap.PROT_READ) # put file in swap
with gzip.GzipFile(mode='r', fileobj=mappedFile) as gfh:
for line in gfh:
lineCount = lineCount + 1
vepResult = json.loads(line.rstrip())
vepParser.set_annotation(copy.deepcopy(vepResult))
vepInputStr = vepParser.get('input')
entry = VcfEntryParser(vepInputStr)
# there are json formatting issues w/the input str
# so replace w/the parsed entry; which is now a dict
vepResult['input'] = entry.get_entry()
refSnpId = entry.get_refsnp()
if not resume:
if previousSnp == args.resumeAfter:
warning(previousSnp,
refSnpId,
file=lfh,
flush=True)
warning("Resuming after:",
args.resumeAfter,
"- SKIPPED",
skipCount,
"lines.",
file=lfh,
flush=True)
resume = True
else:
previousSnp = refSnpId
skipCount = skipCount + 1
continue
if lineCount == 1 or variantCount % args.commitAfter == 0:
warning('Processing new copy object',
file=lfh,
flush=True)
tstart = datetime.now()
vepParser.set('ref_snp_id', refSnpId)
refAllele = entry.get('ref')
altAllele = entry.get('alt').split(',')
chrom = xstr(entry.get('chrom'))
if chrom == 'MT':
chrom = 'M'
position = int(entry.get('pos'))
isMultiAllelic = len(altAllele) > 1
try:
vepParser.set('is_multi_allelic', isMultiAllelic)
vepParser.set('ref_allele', refAllele)
vepParser.set('alt_allele', altAllele)
frequencies = get_frequencies(vepParser, lfh)
vepParser.adsp_rank_and_sort_consequences()
# for each allele
for alt in altAllele:
variantCount = variantCount + 1
metaseqId = ':'.join(
(chrom, xstr(position), refAllele, alt))
positionEnd = entry.infer_variant_end_location(alt)
binIndex = indexer.find_bin_index(
chrom, position, positionEnd)
# NOTE: VEP uses normalized alleles to indicate variant_allele
nRef, nAlt = entry.normalize_alleles(
refAllele, alt, snvDivMinus=True)
alleleFreq = None if frequencies is None \
else get_allele_frequencies(nAlt, frequencies)
msConseq = get_most_severe_consequence(
nAlt, vepParser)
valueStr = '#'.join(
('chr' + xstr(chrom), xstr(position),
xstr(vepParser.get('is_multi_allelic')),
binIndex, refSnpId, metaseqId,
json2str(alleleFreq), json2str(msConseq),
json2str(
get_adsp_ranked_allele_consequences(
nAlt, vepParser)),
json.dumps(vepResult), algInvocId))
copyObj.write(valueStr + '\n')
if variantCount % args.logAfter == 0 \
and variantCount % args.commitAfter != 0:
warning("PARSED",
variantCount,
file=lfh,
flush=True)
if variantCount % args.commitAfter == 0:
tendw = datetime.now()
warning('Copy object prepared in ' +
str(tendw - tstart) + '; ' +
str(copyObj.tell()) +
' bytes; transfering to database',
file=lfh,
flush=True)
copyObj.seek(0)
cursor.copy_from(copyObj,
'variant',
sep='#',
null="NULL",
columns=VARIANT_COLUMNS)
message = '{:,}'.format(variantCount)
if args.commit:
database.commit()
message = "COMMITTED " + message
else:
database.rollback()
message = "PARSED " + message + " -- rolling back"
if variantCount % args.logAfter == 0:
warning(message,
"; up to = ",
refSnpId,
file=lfh,
flush=True)
tend = datetime.now()
warning('Database copy time: ' +
str(tend - tendw),
file=lfh,
flush=True)
warning(' Total time: ' +
str(tend - tstart),
file=lfh,
flush=True)
if args.test:
die("Test complete")
copyObj = io.StringIO() # reset io string
except Exception as e:
warning("ERROR parsing variant",
refSnpId,
file=lfh,
flush=True)
warning(lineCount, ":", line, file=lfh, flush=True)
warning(str(e), file=lfh, flush=True)
raise
# final commit / leftovers
copyObj.seek(0)
cursor.copy_from(copyObj,
'variant',
sep='#',
null="NULL",
columns=VARIANT_COLUMNS)
message = '{:,}'.format(variantCount)
if args.commit:
database.commit()
message = "DONE - COMMITTED " + message
else:
database.rollback()
message = "DONE - PARSED " + message + " -- rolling back"
warning(message, file=lfh, flush=True)
mappedFile.close()
database.close()
indexer.close()
lfh.close()
def load_annotation():
''' extract basic SNP information from VCF line; check against AnnotatedDB; if missing
load '''
indexer = BinIndex(args.gusConfigFile, verbose=False)
database = Database(args.gusConfigFile)
database.connect()
lineCount = 0
variantCount = 0
with database.cursor() as cursor:
with open(args.vcfFile, 'r') as fh:
with open(args.logFileName, 'w') as lfh:
warning("Parsing", args.vcfFile, file=lfh, flush=True)
for line in fh:
lineCount = lineCount + 1
vepResult = {} # will just be the input string, so it matches the annotated variants
if line.startswith('#'):
continue
entry = VcfEntryParser(line.rstrip())
# there are json formatting issues w/the input str
# so replace w/the parsed entry; which is now a dict
vepResult['input'] = entry.get_entry()
refAllele = entry.get('ref')
altAllele = entry.get('alt') # assuming not multiallelic
if refAllele == '0': # happens sometimes
refAllele = '?'
if altAllele == '0':
altAllele = '?'
# truncatedRef = truncate(refAllele, 20)
# truncatedAlt = truncate(altAllele, 20)
chrom = xstr(entry.get('chrom'))
if chrom == 'MT':
chrom = 'M'
position = int(entry.get('pos'))
# metaseqId = ':'.join((chrom, xstr(position), truncatedRef, truncatedAlt))
isMultiAllelic = False # assuming b/c of how the VCF files were generated
metaseqId = ':'.join((chrom, xstr(position), refAllele, altAllele))
try:
if variant_is_missing(database, 'chr' + chrom, metaseqId):
warning(metaseqId, "- MISSING -- LOADING", file=lfh, flush=True)
variantCount = variantCount + 1
positionEnd = entry.infer_variant_end_location(altAllele)
binIndex = indexer.find_bin_index(chrom, position, positionEnd)
cursor.execute(INSERT_SQL,
('chr' + chrom,
position,
isMultiAllelic,
binIndex,
metaseqId,
json.dumps(vepResult),
algInvocId))
if args.commit:
database.commit()
else:
database.rollback()
if lineCount % 50 == 0:
warning("Parsed", lineCount, "lines.", file=lfh, flush=True)
warning("Loaded", variantCount, "missing variants", file=lfh, flush=True)
except Exception:
warning("ERROR parsing variant", metaseqId, file=lfh, flush=True)
warning(lineCount, ":", line, file=lfh, flush=True)
print("FAIL", file=sys.stdout)
raise
warning("DONE - Loaded", variantCount, "missing variants", file=lfh, flush=True)
database.close()
indexer.close()
def load_annotation(chromosome):
''' extract basic SNP information from VCF line; check against AnnotatedDB; if missing
load '''
indexer = BinIndex(args.gusConfigFile, verbose=False)
database = Database(args.gusConfigFile)
database.connect()
fname = '00-All.MT.vcf.gz' if chromosome == 'M' \
else '00-All.' + xstr(chromosome) + '.vcf.gz'
logFname = path.join(args.logDir, fname + '.log')
fname = path.join(args.dir, fname)
lineCount = 0
variantCount = 0
warning("Parsing", fname)
warning("Logging:", logFname)
with database.cursor() as cursor:
with open(fname, 'r') as fhandle, open(logFname, 'w') as lfh:
warning("Parsing", fname, file=lfh, flush=True)
mappedFile = mmap.mmap(fhandle.fileno(), 0,
prot=mmap.PROT_READ) # put file in swap
with gzip.GzipFile(mode='r', fileobj=mappedFile) as gfh:
for line in gfh:
lineCount = lineCount + 1
vepResult = {
} # will just be the input string, so it matches the annotated variants
if line.startswith('#'):
continue
entry = VcfEntryParser(line.rstrip())
# there are json formatting issues w/the input str
# so replace w/the parsed entry; which is now a dict
vepResult['input'] = entry.get_entry()
refSnpId = entry.get_refsnp()
refAllele = entry.get('ref')
altAllele = entry.get('alt').split(',')
if '.' not in altAllele:
if lineCount % 25000 == 0:
warning("Parsed",
lineCount,
"lines.",
file=lfh,
flush=True)
continue # sanity check/all missing are lacking alt alleles
chrom = xstr(entry.get('chrom'))
position = int(entry.get('pos'))
isMultiAllelic = len(altAllele) > 1
try:
if variant_is_missing(database, 'chr' + chrom,
refSnpId):
warning(refSnpId,
"- MISSING -- LOADING",
file=lfh,
flush=True)
for alt in altAllele:
if alt == '.': # checking again in case some are multiallelic
alt = '?'
variantCount = variantCount + 1
metaseqId = ':'.join(
(chrom, xstr(position), refAllele, alt))
positionEnd = entry.infer_variant_end_location(
alt)
binIndex = indexer.find_bin_index(
chrom, position, positionEnd)
cursor.execute(
INSERT_SQL,
('chr' + chrom, xstr(position),
isMultiAllelic,
binIndex, refSnpId, metaseqId,
json.dumps(vepResult), algInvocId))
if args.commit:
database.commit()
else:
database.rollback()
if lineCount % 25000 == 0:
warning("Parsed",
lineCount,
"lines.",
file=lfh,
flush=True)
warning("Loaded",
variantCount,
"missing variants",
file=lfh,
flush=True)
except Exception:
warning("ERROR parsing variant",
refSnpId,
file=lfh,
flush=True)
warning(lineCount, ":", line, file=lfh, flush=True)
raise
if not args.commit:
database.rollback()
warning("DONE -- rolling back")
mappedFile.close()
database.close()
indexer.close()
warning("DONE - Loaded",
variantCount,
"missing variants",
file=lfh,
flush=True)
def update_variant_records_from_vcf():
''' lookup and update variant records from a VCF file
assuming the load by file was called by a plugin, so this variant has already been
verified to be new to the resource; no need to check alternative metaseq IDs'''
cupdater = CADDUpdater(args.logFile, args.databaseDir)
database = Database(args.gusConfigFile)
database.connect()
lineCount = 0
with database.cursor() as updateCursor, \
open(args.vcfFile, 'r') as fh:
try:
for line in fh:
if line.startswith("#"):
continue
lineCount = lineCount + 1
entry = VcfEntryParser(line.rstrip())
refAllele = entry.get('ref')
altAllele = entry.get('alt')
chrom = xstr(entry.get('chrom'))
if chrom == 'MT':
chrom = 'M'
position = int(entry.get('pos'))
metaseqId = ':'.join(
(chrom, xstr(position), refAllele, altAllele))
record = {"metaseq_id": metaseqId} # mimic "record"
if len(refAllele) > 1 or len(altAllele) > 1: # only doing SNVs
update_variant_record(record, cupdater, INDEL)
else:
update_variant_record(record, cupdater, SNV)
if lineCount % args.commitAfter == 0:
warning("Processed:",
lineCount,
"- SNVs:",
cupdater.get_update_count(SNV),
"- INDELS:",
cupdater.get_update_count(INDEL),
" - Not Matched:",
cupdater.get_not_matched_count(),
file=cupdater.lfh(),
flush=True)
updateCursor.execute(cupdater.sql_buffer_str())
if args.commit:
database.commit()
else:
database.rollback()
cupdater.clear_update_sql()
if cupdater.buffered_variant_count() > 0: # trailing
updateCursor.execute(cupdater.sql_buffer_str())
if args.commit:
database.commit()
else:
database.rollback()
warning("DONE - Updated SNVs:",
cupdater.get_update_count(SNV),
"- Updated INDELS:",
cupdater.get_update_count(INDEL),
"- Not Matched:",
cupdater.get_not_matched_count(),
file=cupdater.lfh(),
flush=True)
cupdater.close_lfh()
except Exception as e:
warning(e, entry, file=cupdater.lfh(), flush=True)
database.rollback()
database.close()
print("FAIL", file=sys.stdout)
raise
def update_variant_records(chromosome):
chrLabel = 'chr' + xstr(chromosome)
logFileName = path.join(args.logFilePath, chrLabel + '.log')
cupdater = CADDUpdater(logFileName, args.databaseDir)
cupdater.setChrm(chrLabel)
selectSQL = "SELECT metaseq_id, cadd_scores FROM Variant_" + chrLabel
database = Database(args.gusConfigFile)
database.connect()
lineCount = 0
updateCount = 0
updateIndelCount = 0
skipCount = 0
with database.cursor("RealDictCursor") as selectCursor, \
database.cursor() as updateCursor:
try:
warning("Fetching",
chrLabel,
"variants",
file=cupdater.lfh(),
flush=True)
selectCursor.execute(selectSQL)
warning("DONE - Fetching", file=cupdater.lfh(), flush=True)
for record in selectCursor:
if args.debug and args.veryVerbose:
warning(record, file=cupdater.lfh(), flush=True)
if record['cadd_scores'] is not None:
if args.debug and args.veryVerbose:
warning("Skipping",
record['metaseq_id'],
file=cupdater.lfh(),
flush=True)
skipCount = skipCount + 1
continue
lineCount = lineCount + 1
metaseqId = record['metaseq_id']
chrm, position, refAllele, altAllele = metaseqId.split(':')
if len(refAllele) > 1 or len(altAllele) > 1: # only doing SNVs
update_variant_record(record, cupdater, INDEL)
else:
update_variant_record(record, cupdater, SNV)
if cupdater.get_total_update_count(
) % args.commitAfter == 0 and cupdater.buffered_variant_count(
) > 0:
if args.commit:
if args.debug:
warning("Starting Update",
file=cupdater.lfh(),
flush=True)
updateCursor.execute(cupdater.sql_buffer_str())
if args.debug:
warning("Done", file=cupdater.lfh(), flush=True)
cupdater.clear_update_sql()
database.commit()
else:
database.rollback()
warning(metaseqId,
"- Processed:",
lineCount,
"- SNVs:",
cupdater.get_update_count(SNV),
"- INDELS:",
cupdater.get_update_count(INDEL),
"- Skipped:",
skipCount,
" - Not Matched:",
cupdater.get_not_matched_count(),
file=cupdater.lfh(),
flush=True)
if cupdater.buffered_variant_count() > 0:
updateCursor.execute(cupdater.sql_buffer_str())
if args.commit: # trailing
database.commit()
else:
database.rollback()
warning("DONE - Updated SNVs:",
cupdater.get_update_count(SNV),
"- Updated INDELS:",
cupdater.get_update_count(INDEL),
"- Skipped",
skipCount,
"- Not Matched:",
cupdater.get_not_matched_count(),
file=cupdater.lfh(),
flush=True)
cupdater.close_lfh()
except Exception as e:
warning(e, file=cupdater.lfh(), flush=True)
if args.commit:
database.commit()
else:
database.rollback()
database.close()
raise
database.close()
parser.add_argument('-r', '--rankingFile', required=True,
help="full path to ADSP VEP consequence ranking file")
parser.add_argument('--commit', action='store_true', help="run in commit mode", required=False)
parser.add_argument('--gusConfigFile',
help="full path to gus config file, else assumes $GUS_HOME/config/gus.config")
parser.add_argument('--skipVerification', help="skip check against DB (for avoiding duplications")
parser.add_argument('--verbose', action='store_true')
args = parser.parse_args()
VARIANT_COLUMNS = qw('chromosome location bin_index metaseq_id allele_frequencies adsp_most_severe_consequence adsp_ranked_consequences vep_output row_algorithm_id', returnTuple=True)
algInvocation = AlgorithmInvocation('load_vep_result.py', json.dumps(vars(args)), args.commit, args.gusConfigFile)
algInvocId = xstr(algInvocation.getAlgorithmInvocationId())
algInvocation.close()
warning("Algorithm Invocation ID", algInvocId)
vepParser = VepJsonParser(args.rankingFile, verbose=True)
indexer = BinIndex(args.gusConfigFile, verbose=False)
database = Database(args.gusConfigFile)
database.connect()
load_annotation()
database.close()
indexer.close()
print(algInvocId, file=sys.stdout)
def __get_db_handle(self, gusConfigFile):
''' create database connection '''
self._database = Database(gusConfigFile)
self._database.connect()