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_microbes_online_genome_info(filename):
"""
Read a genomeInfo.txt file from microbes online.
Return a list of gene objects.
"""
with open(filename, 'r') as f:
# we'll be making and returning a list of gene objects
genes = []
# read header and create map from column name to index
# these files have these columns: locusId, accession, GI, scaffoldId, start, stop, strand,
# sysName, name, desc, COG, COGFun, COGDesc, TIGRFam, TIGRRoles, GO, EC, ECDesc
column_names = f.next().rstrip("\n").split("\t")
column = { column_names[index]:index for index in range(0,len(column_names)) }
for line in f:
fields = line.rstrip("\n").split("\t")
# create an object for each row
gene = OpenStruct()
for column_name in column_names:
gene[column_name] = fields[ column[column_name] ]
genes.append(gene)
return genes
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_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_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_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_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_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_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
def read_go_terms(filename):
"""
Read a file of GO (gene ontology) terms and return a list of term objects.
Based on the ontology file OBO v1.2 downloaded from http://www.geneontology.org/.
format-version: 1.2
date: 27:10:2011 14:45
saved-by: gwg
auto-generated-by: OBO-Edit 2.1-rc2
remark: cvs version: $Revision: 1.2357 $
keys are in { id, alt_id,
name, namespace,
def, comment,
created_by, creation_date,
is_obsolete, replaced_by, consider,
synonym, is_a, subset, disjoint_from, relationship, intersection_of,
xref }
"""
# See format description: http://www.geneontology.org/GO.format.obo-1_2.shtml#S.1.1
# Tag-Value Pairs:
# <tag>: <value> {<trailing modifiers>} ! <comment>
# Trailing Modifiers
# {<name>=<value>, <name=value>, <name=value>}
# we'll be making and returning a list of term objects
terms = []
with open(filename, 'r') as f:
in_term_stanza = False
# match quoted string values
quoted_string_re = re.compile(r'"((?:[^"\\]|\\.)*)"(?:\s+(.*?))?')
for line in f:
line = line.rstrip("\n")
if in_term_stanza:
if line=="":
# blank line ends stanza
in_term_stanza = False
else:
# capture a key/value pair
[key,rest] = line.split(': ',1)
# remove comments
comment_index = rest.rfind(' ! ')
if comment_index > -1:
value = rest[0:comment_index]
else:
value = rest
# deal with quoted strings
# here, we're implicitely dropping suffixes from synonym and def
# lines that look like these:
# EXACT [GOC:obol]
# EXACT [EC:4.1.1.18]
# BROAD [EC:1.1.5.4]
# NARROW [EC:2.7.8.7]
# [GOC:bf, GOC:signaling, PMID:15084302, PMID:17662591]
m = quoted_string_re.match(value)
if m:
value = m.group(1)
term.set_or_append(key,value)
elif line=="[Term]":
in_term_stanza = True
term = OpenStruct()
terms.append(term)
return terms