def get_theme_ids(cursor, ensembl_db_name, config_reader, theme_name):
path = config_reader.get_path("resources")
fnm = path + "/" + theme_name + ".txt"
if not os.path.exists(fnm):
print fnm, "not found"
exit(1)
if not os.path.getsize(fnm) > 0:
print fnm, "empty"
exit(1)
switch_to_db(cursor, ensembl_db_name["homo_sapiens"])
inf = erropen(fnm, "r")
gene_ids = []
for line in inf:
line = line.rstrip()
fields = line.split()
stable_id = fields[0]
qry = "select gene_id, description from gene where stable_id='%s'" % stable_id
rows = search_db(cursor, qry)
if not rows:
continue
if "ERROR" in rows[0]:
print rows[0]
exit(1)
gene_ids.append(int(rows[0][0]))
inf.close()
return gene_ids
def get_complement_ids(cursor, ensembl_db_name, config_reader):
path = config_reader.get_path("resources")
theme_names = [
"telomere_maintenance",
"nonhom_end_joining",
"egfr_signaling",
"cell_cycle_checkpoints",
"genecards_top500",
"wnt_pathway",
"enzymes",
"cell_junction",
"actin_binding",
"cell_junction",
"transcription",
"translation",
"meiosis",
]
theme_id_set = set([])
for theme_name in theme_names:
fnm = path + "/" + theme_name + ".txt"
if not os.path.exists(fnm):
print fnm, "not found"
exit(1)
if not os.path.getsize(fnm) > 0:
print fnm, "empty"
exit(1)
switch_to_db(cursor, ensembl_db_name["homo_sapiens"])
inf = erropen(fnm, "r")
gene_ids = []
for line in inf:
line = line.rstrip()
fields = line.split()
stable_id = fields[0]
qry = "select gene_id, description from gene where stable_id='%s'" % stable_id
rows = search_db(cursor, qry)
if not rows:
continue
if "ERROR" in rows[0]:
print rows[0]
exit(1)
theme_id_set.add(int(rows[0][0]))
inf.close()
switch_to_db(cursor, ensembl_db_name["homo_sapiens"])
human_gene_set = set(get_gene_ids(cursor, biotype="protein_coding", is_known=1))
complement = human_gene_set - theme_id_set
return list(complement)
