Commit 91e60a1c authored by Bertrand  NÉRON's avatar Bertrand NÉRON

fix lot of small bugs

use argparse instead of optparse
raise error when system-id is not specify
parent 7110fefd
......@@ -26,9 +26,11 @@ def replicon_parser(replicon_data):
:rtype: dict
"""
replicon_db = {}
Replicon_info = namedtuple('Replicon_info', ('name', 'taxid', 'strain', 'taxonomy', 'type'))
Replicon_info = namedtuple('Replicon_info', ('name', 'ncbi_id', 'taxid', 'strain', 'taxonomy', 'type'))
with open(replicon_data, 'r') as replicon_file:
line_nb = 0
for line in replicon_file:
line_nb += 1
if not line.startswith('#'):
line = line.strip()
fields = line.split('\t')
......@@ -43,12 +45,13 @@ def replicon_parser(replicon_data):
taxonomy = fields[4].split('; ')
# remove ending dot or semi-colon from the last term of taxonnomy
if taxonomy[-1].endswith('.') or taxonomy[-1].endswith(';'):
taxonomy[-1] = taxonomy[-1][:-1]
taxonomy = taxonomy[-1][:-1]
replicon_type = fields[5]
replicon_db[replicon_id] = Replicon_info(replicon_id, ncbi_id, taxid, strain,
taxonomy, replicon_type)
except Exception as err:
raise Exception("Error during parsing line : {0} : {1}".format(line, err))
raise Exception("Error during parsing line {0}: {1} : {2}".format(line_nb, line, err))
return replicon_db
def system_parser(system_data):
......@@ -66,32 +69,39 @@ def system_parser(system_data):
'score', 'i_evalue', 'coverage', 'match_begin', 'match_end', 'name', 'description')
)
with open(system_data, 'r') as system_file :
with open(system_data, 'r') as system_file:
line_nb = 0
for line in system_file:
line_nb += 1
if line[0] != '#':
line = line.strip()
fields = line.split('\t')
gene_code = fields[0]
if gene_code in system_db:
raise KeyError("duplicate replicon:" + fields[0])
gene_id = fields[1]
protein_length = int(fields[2])
strand = fields[3] if fields[3] != '-' else None
begin = int(fields[4]) if fields[4] != '-' else None
end = int(fields[5]) if fields[5] != '-' else None
match = fields[6] if fields[6] != '-' else None
# in old data, float number use , instead of dot
score = float(fields[7].replace(',', '.')) if fields[7] != '-' else None
i_evalue = float(fields[8].replace(',', '.')) if fields[8] != '-' else None
coverage = float(fields[9].replace(',', '.')) if fields[9] != '-' else None
match_begin = int(fields[10]) if fields[10] != '-' else None
match_end = int(fields[11]) if fields[11] != '-' else None
replicon_id = fields[12]
predicted_system = fields[13] if fields[13] != '-' else None
system_id = fields[14] if fields[14] != '-' else None
system_status = fields[15] if fields[15] != '-' else None
gene_name = fields[16] if fields[16] else None
description = fields[17] if fields[17] else None
try:
gene_id = fields[1]
protein_length = int(fields[2])
strand = fields[3] if fields[3] != '-' else None
begin = int(fields[4]) if fields[4] != '-' else None
end = int(fields[5]) if fields[5] != '-' else None
match = fields[6] if fields[6] != '-' else None
# in old data, float number use , instead of dot
score = float(fields[7].replace(',', '.')) if fields[7] != '-' else None
i_evalue = float(fields[8].replace(',', '.')) if fields[8] != '-' else None
coverage = float(fields[9].replace(',', '.')) if fields[9] != '-' else None
match_begin = int(fields[10]) if fields[10] != '-' else None
match_end = int(fields[11]) if fields[11] != '-' else None
replicon_id = fields[12]
predicted_system = fields[13] if fields[13] != '-' else None
system_id = fields[14]
if system_id == '-':
raise RuntimeError("System-Id is empty")
system_status = fields[15] if fields[15] != '-' else None
gene_name = fields[16] if fields[16] else None
description = fields[17] if fields[17] else None
except Exception as err:
raise RuntimeError("Error during parsing line {0}: {1} : {2}".format(line_nb, line, err))
gene = Gene(gene_code,
gene_id,
protein_length,
......@@ -182,7 +192,6 @@ def fill_db(server_uri, db_name, user, passwd, replicon_db, system_db, force_upd
secretion_system.genes = genes
secreton_db.save_doc(secretion_system, force_update=force_update)
if __name__ == '__main__':
import argparse
import sys
......@@ -194,7 +203,7 @@ if __name__ == '__main__':
return user, password
usage = """
%prog [options]
%(prog)s [options]
parse a file containing replicon informations and a file containing system informations
and fill a couchDB data base with these informations
"""
......@@ -202,23 +211,19 @@ if __name__ == '__main__':
server_opt = parser.add_argument_group(title="Server Options")
server_opt.add_argument("-S", "--server",
action="store",
type="string",
dest="server_url",
help="the url of the couchDB server (with the port)")
server_opt.add_argument("-d", "--database",
action="store",
type="string",
dest="db_name",
help="the name of the data base")
parsing_opt = parser.add_argument_group(title="Parsing Options")
parsing_opt.add_argument("-r", "--replicon",
action="store",
type="string",
dest="replicon_path",
help="the path to the replicon file to parse")
parsing_opt.add_argument("-s", "--system",
action="store",
type="string",
dest="system_path",
help="the path to the system secretion file to parse")
parsing_opt.add_argument("-f", "--force_update",
......@@ -226,43 +231,41 @@ if __name__ == '__main__':
dest="force_update",
default=False,
help="insert document even if there is already a document with the same id (replace it)")
options, args = parser.parse_args()
args = parser.parse_args()
if not options.server_url:
if not args.server_url:
print("You must specify a server url", file=sys.stderr)
parser.print_help(sys.stderr)
sys.exit(1)
if not options.db_name:
if not args.db_name:
print("You must specify a data base name", file=sys.stderr)
parser.print_help(sys.stderr)
sys.exit(1)
if not options.replicon_path:
if not args.replicon_path:
print("You must specify the path to the replicon information file", file=sys.stderr)
parser.print_help(sys.stderr)
sys.exit(1)
if not options.system_path:
if not args.system_path:
print("You must specify the path to the secretion system information file", file=sys.stderr)
parser.print_help(sys.stderr)
sys.exit(1)
replicon_db = replicon_parser(options.replicon_path)
system_db = system_parser(options.system_path)
replicon_db = replicon_parser(args.replicon_path)
system_db = system_parser(args.system_path)
try_again = 0
while True:
user, password = get_credentials()
try:
fill_db(options.server_url, options.db_name, user, password,
replicon_db, system_db, force_update=options.force_update)
fill_db(args.server_url, args.db_name, user, password,
replicon_db, system_db, force_update=args.force_update)
break
except restkit.errors.Unauthorized as err:
print("Bad authentication, try again", file=sys.stderr)
try_again += 1
if try_again > 2:
sys.exit("Authentication failure")
except Exception, err:
print(err, file=sys.stderr)
except Exception as err:
sys.exit(2)
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