def read_cog_categories(filename):
"""
Read COG functional categories (see http://www.ncbi.nlm.nih.gov/COG/grace/fiew.cgi)
"""
cog_categories = []
parent = None
with open(filename, 'r') as f:
for line in f:
c = OpenStruct()
if re.match("[A-Z]\t.*", line):
fields = line.rstrip("\n").split("\t")
c.id = fields[0]
c.name = fields[3]
c.parents = (parent,)
c.namespace = "cog subcategory"
else:
c.name = line.rstrip("\n")
c.namespace = "cog category"
parent = c.name
cog_categories.append(c)
return cog_categories
def read_cog_categories(filename):
"""
Read COG functional categories (see http://www.ncbi.nlm.nih.gov/COG/grace/fiew.cgi)
"""
cog_categories = []
parent = None
with open(filename, 'r') as f:
for line in f:
c = OpenStruct()
if re.match("[A-Z]\t.*", line):
fields = line.rstrip("\n").split("\t")
c.id = fields[0]
c.name = fields[3]
c.parents = (parent,)
c.namespace = "cog subcategory"
else:
c.name = line.rstrip("\n")
c.namespace = "cog category"
parent = c.name
cog_categories.append(c)
return cog_categories
def read_cogs(filename):
"""
Read COG functions.
"""
cog_re = re.compile(r'\[(\w+)\]\s+(COG\d+)\s+(.*)')
cogs = []
with open(filename, 'r') as f:
for line in f:
m = cog_re.match(line)
if m:
cog = OpenStruct()
cog.id = m.group(2)
cog.name = m.group(3)
cog.parents = m.group(1)
cog.namespace = 'cog'
cogs.append(cog)
return cogs
def read_cogs(filename):
"""
Read COG functions.
"""
cog_re = re.compile(r'\[(\w+)\]\s+(COG\d+)\s+(.*)')
cogs = []
with open(filename, 'r') as f:
for line in f:
m = cog_re.match(line)
if m:
cog = OpenStruct()
cog.id = m.group(2)
cog.name = m.group(3)
cog.parents = m.group(1)
cog.namespace = 'cog'
cogs.append(cog)
return cogs
