def align_against_genomes(cur, args, path):
for g in args.chromolist:
output = os.path.abspath(
os.path.join(
args.output,
"{0}_v_{1}.lastz".format(os.path.basename(args.probefile), g)))
target = path.format(g)
prefab = False
if os.path.isfile(output + '.clean'):
inpt = raw_input(
"The output file {0} exists. Do you want to use it [Y/n]? ".
format(g))
if inpt == 'Y' or inpt == 'Yes':
prefab = True
clean = output + '.clean'
else:
prefab = False
if not prefab:
multi_lastz_runner(output, args.cores, target, args.probefile,
False, args.coverage, args.identity)
clean = clean_lastz_data(output)
if args.db:
create_species_lastz_tables(cur, g)
insert_species_to_lastz_tables(cur, g, clean)
cur.execute('INSERT INTO species (name) VALUES (?)', (g, ))
def main():
start_time = time.time()
print 'Started: ', time.strftime("%a %b %d, %Y %H:%M:%S",
time.localtime(start_time))
options, arg = interface()
multi_lastz_runner(options.output, options.nprocs, options.target,
options.query, options.huge, options.coverage,
options.identity, options.size)
end_time = time.time()
print 'Ended: ', time.strftime("%a %b %d, %Y %H:%M:%S",
time.localtime(end_time))
print 'Time for execution: ', (end_time - start_time) / 60, 'minutes'
def main():
start_time = time.time()
print 'Started: ', time.strftime("%a %b %d, %Y %H:%M:%S", time.localtime(start_time))
options, arg = interface()
multi_lastz_runner(
options.output,
options.nprocs,
options.target,
options.query,
options.huge,
options.coverage,
options.identity,
options.size
)
end_time = time.time()
print 'Ended: ', time.strftime("%a %b %d, %Y %H:%M:%S", time.localtime(end_time))
print 'Time for execution: ', (end_time - start_time) / 60, 'minutes'
def align_against_genomes(cur, args, path):
for g in args.chromolist:
output = os.path.abspath(os.path.join(args.output, "{0}_v_{1}.lastz".format(os.path.basename(args.probefile), g)))
target = path.format(g)
prefab = False
if os.path.isfile(output + '.clean'):
inpt = raw_input("The output file {0} exists. Do you want to use it [Y/n]? ".format(g))
if inpt == 'Y' or inpt == 'Yes':
prefab = True
clean = output + '.clean'
else:
prefab = False
if not prefab:
multi_lastz_runner(output, args.cores, target, args.probefile, False, args.coverage, args.identity)
clean = clean_lastz_data(output)
if args.db:
create_species_lastz_tables(cur, g)
insert_species_to_lastz_tables(cur, g, clean)
cur.execute('INSERT INTO species (name) VALUES (?)', (g,))
