def query_go():
"""Query the GO data from MySQL"""
conn = mu.get_conn()
cursor = conn.cursor()
query = "SELECT gene.gid, gene.symbol " "FROM gene " "WHERE gene.source = 'GO'"
cursor.execute(query)
results = cursor.fetchall()
write_table(results)
def map_gene_id(geneid, db=mu.get_conn()):
"""Maps the provided gene id to a gene symbol using the MySQL db"""
cursor = db.cursor()
cmd = ("SELECT gene.symbol "
"FROM gene "
"WHERE gene.source = 'EntrezGene' "
"AND gene.gid = '" + geneid + "'")
cursor.execute(cmd)
return cursor.fetchall()
def process_download(fl='../data/gene2pubmed'):
"""Counts all of the citations for each human gene in the gene2
pubmed file and maps gene ids to gene symbols. Then writes the
results to disk."""
db = mu.get_conn()
curr = ''
count = 0
scores = dict()
with contextlib.nested(open(fl), open('../data/citations.tsv', 'w')) as \
(infile, outfile):
reader = csv.reader(infile, delimiter='\t')
writer = csv.writer(outfile, delimiter='\t')
next(reader, None)
for row in reader:
(taxid, gid, pmid) = row
if taxid != '9606': continue #if wrong species
if curr == '': #if first time human is seen
curr = gid
count = 1
elif gid != curr: #if switching to a new gene id
slist = map_gene_id(curr, db)
for tuple in slist:
symbol = tuple[0].decode()
if symbol not in scores:
scores[symbol] = count
else:
scores[symbol] += count
curr = gid
count = 1
else: #if another publication for the same gene id is seen
count += 1
slist = map_gene_id(curr, db) #for the last human gene
for tuple in slist:
symbol = tuple[0].decode()
if symbol not in scores:
scores[symbol] = count
else:
scores[symbol] += count
for symbol in scores: #write out the results
writer.writerow([symbol, str(scores[symbol])])
