def main():
task.check_conf(["entities", "repositories", "biomart.db"])
conf = task.conf
insert_size = conf.get("biomart.insert_size", DEFAULT_INSERT_SIZE, dtype=int)
db_engine = conf.get("biomart.db.engine", DEFAULT_DB_ENGINE)
log = task.logger()
id_port = task.ports("id")
es = EntityServer(conf["entities"])
em = es.manager()
rs = RepositoryServer(conf["repositories"])
conn = biomart_db_connect(conf["biomart.db"], log)
cursor = conn.cursor()
table_infixs = set(ID_TYPE_TO_TABLE_INFIX.values())
feat_ids = {}
for name in table_infixs:
if name == "gene":
continue
cursor.execute("""
CREATE TABLE IF NOT EXISTS exp_{0}_trs (
{0}_id int(11) NOT NULL,
icdo_id int(11) NOT NULL,
exp_id int(11) NOT NULL,
upreg_total int(11) DEFAULT NULL,
upreg_observed double DEFAULT NULL,
upreg_expected double DEFAULT NULL,
upreg_stdev double DEFAULT NULL,
upreg_pvalue double DEFAULT NULL,
upreg_cpvalue double DEFAULT NULL,
downreg_total int(11) DEFAULT NULL,
downreg_observed double DEFAULT NULL,
downreg_expected double DEFAULT NULL,
downreg_stdev double DEFAULT NULL,
downreg_pvalue double DEFAULT NULL,
downreg_cpvalue double DEFAULT NULL,
PRIMARY KEY ({0}_id,icdo_id,exp_id),
KEY icdo (icdo_id,exp_id),
KEY exp (exp_id),
CONSTRAINT exp_{0}_trs_{0}_id FOREIGN KEY ({0}_id) REFERENCES ent_{0} ({0}_id),
CONSTRAINT exp_{0}_trs_icdo_id FOREIGN KEY (icdo_id) REFERENCES ent_icdo (id),
CONSTRAINT exp_{0}_trs_exp_id FOREIGN KEY (exp_id) REFERENCES ent_experiment (id)
) ENGINE={1} DEFAULT CHARSET=latin1""".format(name, db_engine))
feat_ids[name] = map_from_select(cursor, "SELECT {0}_id, {0}_name FROM ent_{0}".format(name))
icdo = map_from_select(cursor, "SELECT id, icdo_topography_code, icdo_morphology_code FROM ent_icdo")
exp = map_from_select(cursor, "SELECT id, study_id, platf_id FROM ent_experiment")
for id_type, eid in id_port:
e = em.find(eid, types.MRNA_ENRICHMENT)
if e is None:
log.error("{} not found: {1}".format(types.MRNA_ENRICHMENT, eid))
continue
if "results_file" not in e:
log.error("{} [{}] without results file.".format(types.MRNA_ENRICHMENT, eid))
continue
study_id = e["study_id"]
platform_id = e["platform_id"]
icdo_topography = e["icdo_topography"]
icdo_morphology = e["icdo_morphology"]
okey = (study_id, platform_id, icdo_topography, icdo_morphology, id_type)
log.info("Exporting enrichment results ({}) [{}] ...".format(", ".join(okey), eid))
table_infix = ID_TYPE_TO_TABLE_INFIX[id_type]
icdo_key = (icdo_topography, icdo_morphology)
if icdo_key not in icdo:
log.error("ICDO ({}) not found in the database".format(", ".join(icdo_key)))
continue
icdo_id = icdo[icdo_key]
exp_key = (study_id, platform_id)
if exp_key not in exp:
log.error("Experiment ({}) not found in the database".format(", ".join(exp_key)))
continue
exp_id = exp[exp_key]
ib = BatchInsert(cursor, "exp_{}_trs".format(table_infix),
["{}_id".format(table_infix), "icdo_id", "exp_id",
"upreg_total", "upreg_observed", "upreg_expected", "upreg_stdev", "upreg_pvalue", "upreg_cpvalue",
"downreg_total", "downreg_observed", "downreg_expected", "downreg_stdev", "downreg_pvalue", "downreg_cpvalue"], insert_size)
results_repo, results_path = rs.from_url(e["results_file"])
try:
reader = results_repo.open_reader(results_path)
except Exception as ex:
log.exception(ex)
ib.close()
results_repo.close()
continue
# read header
hdr_map = {}
hdr = reader.readline().rstrip().split("\t")
for i, name in enumerate(hdr):
hdr_map[name] = i
try:
col_indices = [hdr_map[x] for x in __COLUMN_NAMES]
except KeyError as e:
log.warn("Column {} not found in results files, most probably because it is empty".format(e.args[0]))
reader.close()
ib.close()
results_repo.close()
continue
skipped_ids = set()
fids = feat_ids[table_infix]
# read data
for line in reader:
line = line.rstrip()
data = line.split("\t")
feat_name = data[0]
data = [data[i] for i in col_indices]
if feat_name not in fids:
skipped_ids.add(feat_name)
continue
feat_id = fids[feat_name]
ib.insert(feat_id, icdo_id, exp_id, *data)
if len(skipped_ids) > 0:
log.warn("There were {} feature names not found:\n{}".format(len(skipped_ids), ",".join(skipped_ids)))
log.debug("{} results inserted".format(ib.count))
ib.close()
reader.close()
em.close()
es.close()
rs.close()
def main():
task.check_conf(["entities", "repositories", "biomart.db"])
conf = task.conf
insert_size = conf.get("biomart.insert_size", DEFAULT_INSERT_SIZE, dtype=int)
db_engine = conf.get("biomart.db.engine", DEFAULT_DB_ENGINE)
log = task.logger()
oncodrive_port = task.ports("id")
es = EntityServer(conf["entities"])
em = es.manager()
rs = RepositoryServer(conf["repositories"])
conn = biomart_db_connect(conf["biomart.db"], log)
cursor = conn.cursor()
gene = map_from_select(cursor, "SELECT id, gene_name FROM ent_gene")
icdo = map_from_select(cursor, "SELECT id, icdo_topography_code, icdo_morphology_code FROM ent_icdo")
exp = map_from_select(cursor, "SELECT id, study_id, platf_id FROM ent_experiment")
cursor.execute(
"""
CREATE TABLE IF NOT EXISTS exp_gene_trs (
gene_id int(11) NOT NULL,
icdo_id int(11) NOT NULL,
exp_id int(11) NOT NULL,
upreg_total int(11) DEFAULT NULL,
upreg_observed double DEFAULT NULL,
upreg_expected double DEFAULT NULL,
upreg_stdev double DEFAULT NULL,
upreg_pvalue double DEFAULT NULL,
upreg_cpvalue double DEFAULT NULL,
downreg_total int(11) DEFAULT NULL,
downreg_observed double DEFAULT NULL,
downreg_expected double DEFAULT NULL,
downreg_stdev double DEFAULT NULL,
downreg_pvalue double DEFAULT NULL,
downreg_cpvalue double DEFAULT NULL,
PRIMARY KEY (gene_id,icdo_id,exp_id),
KEY icdo (icdo_id,exp_id),
KEY exp (exp_id),
CONSTRAINT exp_gene_trs_gene_id FOREIGN KEY (gene_id) REFERENCES ent_gene (id),
CONSTRAINT exp_gene_trs_icdo_id FOREIGN KEY (icdo_id) REFERENCES ent_icdo (id),
CONSTRAINT exp_gene_trs_exp_id FOREIGN KEY (exp_id) REFERENCES ent_experiment (id)
) ENGINE={} DEFAULT CHARSET=latin1""".format(
db_engine
)
)
cursor.execute("LOCK TABLES exp_gene_trs WRITE")
lock_count = 0
for eid in oncodrive_port:
e = em.find(eid, types.MRNA_ONCODRIVE_GENES)
if e is None:
log.error("{} not found: {}".format(types.MRNA_ONCODRIVE_GENES, eid))
continue
if "results_file" not in e:
log.error("{} [{}] without results file.".format(types.MRNA_ONCODRIVE_GENES, eid))
continue
study_id = e["study_id"]
platform_id = e["platform_id"]
icdo_topography = e["icdo_topography"]
icdo_morphology = e["icdo_morphology"]
okey = (study_id, platform_id, icdo_topography, icdo_morphology)
log.info("Exporting oncodrive results ({}) [{}] ...".format(", ".join(okey), eid))
icdo_key = (icdo_topography, icdo_morphology)
if icdo_key not in icdo:
log.error("ICDO ({}) not found in the database".format(", ".join(icdo_key)))
continue
icdo_id = icdo[icdo_key]
exp_key = (study_id, platform_id)
if exp_key not in exp:
log.error("Experiment ({}) not found in the database".format(", ".join(exp_key)))
continue
exp_id = exp[exp_key]
ib = BatchInsert(
cursor,
"exp_gene_trs",
[
"gene_id",
"icdo_id",
"exp_id",
"upreg_total",
"upreg_observed",
"upreg_expected",
"upreg_stdev",
"upreg_pvalue",
"upreg_cpvalue",
"downreg_total",
"downreg_observed",
"downreg_expected",
"downreg_stdev",
"downreg_pvalue",
"downreg_cpvalue",
],
insert_size,
)
results_repo, results_path = rs.from_url(e["results_file"])
try:
reader = results_repo.open_reader(results_path)
except Exception as ex:
log.exception(ex)
ib.close()
results_repo.close()
continue
# read header
hdr_map = {}
hdr = reader.readline().rstrip().split("\t")
for i, name in enumerate(hdr):
hdr_map[name] = i
try:
col_indices = [hdr_map[x] for x in __COLUMN_NAMES]
except KeyError as e:
log.warn("Column {} not found in results files, most probably because it is empty".format(e.args[0]))
reader.close()
lock_count += ib.count
ib.close()
results_repo.close()
continue
skipped_genes = set()
# read data
for line in reader:
line = line.rstrip()
data = line.split("\t")
gene_name = data[0]
data = [data[i] for i in col_indices]
if gene_name not in gene:
skipped_genes.add(gene_name)
continue
gene_id = gene[gene_name]
ib.insert(gene_id, icdo_id, exp_id, *data)
if len(skipped_genes) > 0:
log.warn("There were {} gene names not found:\n{}".format(len(skipped_genes), ",".join(skipped_genes)))
log.debug("{} gene results inserted".format(ib.count))
lock_count += ib.count
ib.close()
reader.close()
if lock_count >= 1000000:
cursor.execute("UNLOCK TABLES")
cursor.execute("OPTIMIZE NO_WRITE_TO_BINLOG TABLE exp_gene_trs")
cursor.execute("LOCK TABLES exp_gene_trs WRITE")
lock_count = 0
cursor.execute("UNLOCK TABLES")
cursor.execute("OPTIMIZE NO_WRITE_TO_BINLOG TABLE exp_gene_trs")
cursor.close()
em.close()
es.close()
rs.close()
