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
def read_tigrfams_by_role(filename):
"""
This is no longer used!
Reads the hierarchical structure of TIGRFams organized into categories called roles.
Returns a nested list structure of roles and sub-roles that hold tigrfams.
Downloaded file from here: http://cmr.jcvi.org/tigr-scripts/CMR/shared/EvidenceList.cgi?ev_type=TIGRFAM&order_type=role
Note the TIGRFams flat file is more complete than the TIGRFams by role file.
"""
# we'll be making and returning a nested list of tigr roles holding tigrfams
tigrfams_by_role = []
with open(filename, 'r') as f:
category = None
subcategory = None
for line in f:
# skip blank lines
if len(line.strip())==0:
continue
if line.startswith(" "):
fields = line.lstrip(' ').rstrip("\n").split("\t")
# skip column headers
if fields[0] == 'Accession':
continue
tigrfam = OpenStruct()
tigrfam.id = fields[0]
tigrfam.name = fields[1]
tigrfam.description = fields[2]
subcategory['tigrfams'].append(tigrfam)
elif line.startswith(" "):
name = line.strip()
subcategory = {'name':name, 'tigrfams':[]}
category['roles'].append(subcategory)
else:
name = line.strip()
category = {'name':name, 'roles':[]}
tigrfams_by_role.append(category)
return tigrfams_by_role
def read_tigrfams_by_role(filename):
"""
This is no longer used!
Reads the hierarchical structure of TIGRFams organized into categories called roles.
Returns a nested list structure of roles and sub-roles that hold tigrfams.
Downloaded file from here: http://cmr.jcvi.org/tigr-scripts/CMR/shared/EvidenceList.cgi?ev_type=TIGRFAM&order_type=role
Note the TIGRFams flat file is more complete than the TIGRFams by role file.
"""
# we'll be making and returning a nested list of tigr roles holding tigrfams
tigrfams_by_role = []
with open(filename, 'r') as f:
category = None
subcategory = None
for line in f:
# skip blank lines
if len(line.strip())==0:
continue
if line.startswith(" "):
fields = line.lstrip(' ').rstrip("\n").split("\t")
# skip column headers
if fields[0] == 'Accession':
continue
tigrfam = OpenStruct()
tigrfam.id = fields[0]
tigrfam.name = fields[1]
tigrfam.description = fields[2]
subcategory['tigrfams'].append(tigrfam)
elif line.startswith(" "):
name = line.strip()
subcategory = {'name':name, 'tigrfams':[]}
category['roles'].append(subcategory)
else:
name = line.strip()
category = {'name':name, 'roles':[]}
tigrfams_by_role.append(category)
return tigrfams_by_role
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_tigrfams(filename):
"""
Read the flat listing of TIGRFams.
Note the TIGRFams flat file is more complete than the TIGRFams by role file.
The flat file is a superset of the by-role file.
"""
tigrfams = []
with open(filename, 'r') as f:
#skip header
line = f.next()
for line in f:
fields = line.rstrip("\n").split("\t")
tigrfam = OpenStruct()
tigrfam.id = fields[0]
tigrfam.name = fields[1]
tigrfam.description = fields[2]
tigrfams.append(tigrfam)
return tigrfams
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_tigrfams(filename):
"""
Read the flat listing of TIGRFams.
Note the TIGRFams flat file is more complete than the TIGRFams by role file.
The flat file is a superset of the by-role file.
"""
tigrfams = []
with open(filename, 'r') as f:
#skip header
line = f.next()
for line in f:
fields = line.rstrip("\n").split("\t")
tigrfam = OpenStruct()
tigrfam.id = fields[0]
tigrfam.name = fields[1]
tigrfam.description = fields[2]
tigrfams.append(tigrfam)
return tigrfams
