def read_tigr_roles(filename):
"""
Reads a truly loony file format that stores the tigrfam mainrole/subrole hierarchy.
Returns a tuple containing a list of mainroles whose children are subroles and
a dictionary from tigr role id to tigr roles, which can be used with the file
TIGRFAMS_ROLE_LINK to attach TIGRFams to roles.
"""
mainroles = []
mainroles_by_name = {}
mainroles_by_id = {}
roles_by_id = {}
with open(filename, 'r') as f:
for line in f:
fields = line.rstrip("\n").split("\t")
role = OpenStruct()
role.tigr_role_id = int(fields[1])
role.type = fields[2].rstrip(':')
role.name = fields[3]
if role.type=='mainrole':
if role.name not in mainroles_by_name:
mainroles.append(role)
mainroles_by_name[role.name] = role
role.children = []
mainroles_by_id[role.tigr_role_id] = mainroles_by_name[role.name]
elif role.type=='sub1role':
roles_by_id[role.tigr_role_id] = role
else:
raise "Unknown role type: " + role.type
# add subroles to main roles
for id in roles_by_id:
mainroles_by_id[id].children.append(roles_by_id[id])
return (mainroles, roles_by_id,)
def read_tigr_roles(filename):
"""
Reads a truly loony file format that stores the tigrfam mainrole/subrole hierarchy.
Returns a tuple containing a list of mainroles whose children are subroles and
a dictionary from tigr role id to tigr roles, which can be used with the file
TIGRFAMS_ROLE_LINK to attach TIGRFams to roles.
"""
mainroles = []
mainroles_by_name = {}
mainroles_by_id = {}
roles_by_id = {}
with open(filename, 'r') as f:
for line in f:
fields = line.rstrip("\n").split("\t")
role = OpenStruct()
role.tigr_role_id = int(fields[1])
role.type = fields[2].rstrip(':')
role.name = fields[3]
if role.type=='mainrole':
if role.name not in mainroles_by_name:
mainroles.append(role)
mainroles_by_name[role.name] = role
role.children = []
mainroles_by_id[role.tigr_role_id] = mainroles_by_name[role.name]
elif role.type=='sub1role':
roles_by_id[role.tigr_role_id] = role
else:
raise "Unknown role type: " + role.type
# add subroles to main roles
for id in roles_by_id:
mainroles_by_id[id].children.append(roles_by_id[id])
return (mainroles, roles_by_id,)
