def genbank_view(params):
for param in params:
altname = resolve_fname(param.acc, format="gb")
if os.path.isfile(param.acc):
stream = utils.gz_read(param.acc)
elif os.path.isfile(altname):
stream = utils.gz_read(altname)
else:
stream = []
utils.error(f"data not found: {param.acc}")
for line in stream:
print(line, end='')
def parse_data(fname, study_size=10):
"""
Take a .gaf file and return an association dictionary and population dict.
"""
if not os.path.isfile(fname):
utils.error("Association file needs to be downloaded first.")
# Read the population from file
association = {}
population = set()
stream = utils.gz_read(fname, 'r')
print(f"*** parsing {fname}")
# Get the gene from each row
for line in stream:
line = line.decode()
if line.startswith('!'):
continue
gene = line.split('\t')[2]
goterm = line.split('\t')[4]
association.setdefault(gene, set()).update([goterm])
population.update([gene])
return population, association
def read_json_file(fname):
"""
Returns the content of a JSON file.
"""
fp = utils.gz_read(fname)
data = json.load(fp)
fp.close()
return data
