def __open(self): self.__f = tsv.open(self.path) self.line_num = 0 if self.header: tsv.skip_comments_and_empty(self.__f)
def fetch_iter(db, muts_path, maps=None, predictors=None, muts_header=False, state=None, logger=None):
"""
Iterator that fetches scores from the database from the mutations in a file.
:param db: FannsDb interface.
:param muts_path: The input path for mutations.
:param maps: Map transcript/protein ensembl identifiers with external identifiers (swissprot_id, ...)
:param predictors: Predictors for which to obtain the scores.
:param muts_header: Whether the muts_path has a header or not.
:param state: The state of the iteration: hits, fails.
:param logger: Logger to use. If not specified a new one is created.
"""
def query_mutation(logger, db, mut, maps, predictors):
if mut.coord == Mutation.GENOMIC:
if logger.isEnabledFor(logging.DEBUG):
logger.debug(" Querying {} {} {} {} {} {} {} ...".format(
mut.chr, mut.start, mut.end or "*", mut.ref or "*", mut.alt, mut.strand or "*", mut.identifier or "*"))
for row in db.query_scores(chr=mut.chr, start=mut.start,
ref=mut.ref, alt=mut.alt, strand=mut.strand,
predictors=predictors, maps=maps):
yield row
elif mut.coord == Mutation.PROTEIN:
if logger.isEnabledFor(logging.DEBUG):
logger.debug(" Querying {} {} {} {} {} ...".format(
mut.protein, mut.start, mut.ref or "*", mut.alt, mut.identifier or "*"))
for row in db.query_scores(protein=mut.protein, aa_pos=mut.start, aa_ref=mut.ref, aa_alt=mut.alt,
predictors=predictors, maps=maps):
yield row
else:
logger.warn("Unknown coordinates system: {}".format(mut.line))
if logger is None:
logger = logging.getLogger("fannsdb.fetch")
state = state if state is not None else {}
state[STATE_HITS] = state[STATE_FAILS] = 0
maps = maps if maps is not None else []
predictors = predictors if predictors is not None else []
logger.info("Reading {} ...".format(os.path.basename(muts_path) if muts_path != "-" else "from standard input"))
progress = RatedProgress(logger, name="SNVs")
with tsv.open(muts_path) as f:
if muts_header:
tsv.skip_comments_and_empty(f) # this returns the first non empty nor comment line (the header)
mutparser = DnaAndProtMutationParser()
for line_num, line in enumerate(f, start=1):
line = line.rstrip(" \n\r")
if len(line) == 0 or line.startswith("#"):
continue
try:
mut = mutparser.parse(line)
except PrematureEnd:
logger.error("Missing fields at line {}".format(line_num))
state[STATE_FAILS] += 1
continue
except UnexpectedToken as ex:
logger.error("Unexpected field '{}' at line {}".format(ex.args[0], line_num))
state[STATE_FAILS] += 1
continue
state.update({
STATE_LINE_NUM : line_num,
STATE_LINE : line,
STATE_MUTATION : mut})
exists = False
for row in query_mutation(logger, db, mut, maps, predictors):
exists = True
yield row
progress.update()
if exists:
state[STATE_HITS] += 1
else:
state[STATE_FAILS] += 1
progress.log_totals()
hits, fails = [state[k] for k in [STATE_HITS, STATE_FAILS]]
logger.info("Finished. total={}, hits={}, fails={}, elapsed={}".format(hits + fails, hits, fails, progress.elapsed_time))
