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,)
def read_genes(filename, chromosome=None, chromosome_map=None, rna=False):
genes = []
with open(filename, 'r') as f:
try:
# first two lines hold title and column headers:
title = f.next()
# figure out chromosome from title
if chromosome is None:
for key in chromosome_map:
if title.find(key) > -1:
chromosome = chromosome_map[key]
break
if chromosome is None:
raise Exception(
"Can't figure out chromosome for: %s\ntitle=%s", filename,
title)
# parse out column headers
columns = {}
i = 0
for column in f.next().strip().split("\t"):
columns[column] = i
i += 1
except Exception as e:
print "Error reading file: " + filename
print str(type(e)) + ": " + str(e)
return None
try:
# read line into objects
for line in f:
# strip leading and trailing whitespace
line = line.strip()
# skip blank lines
if (len(line) == 0): continue
fields = line.split("\t")
gene = OpenStruct()
gene.name = fields[columns['Locus_tag']] # locus tag
if (fields[columns['Locus']] != '-'):
gene.common_name = fields[columns['Locus']] # locus
if 'Gi' in columns:
gene.gi = int(fields[columns['Gi']])
gene.geneid = int(fields[columns['GeneID']])
gene.strand = fields[columns['Strand']] # '+' or '-'
gene.start = int(fields[columns['Start']])
gene.end = int(fields[columns['End']])
if (fields[columns['Product Name']] != '-'):
gene.description = fields[columns['Product Name']] # locus
gene.chromosome = chromosome
if rna:
gene.type = guess_rna_gene_type(gene.description)
else:
gene.type = 'CDS'
genes.append(gene)
except Exception as e:
print "Error reading line: " + line
print str(type(e)) + ": " + str(e)
return genes