def bgzip_and_tabix(cnf, vcf_fpath, tabix_parameters='', **kwargs):
gzipped_fpath = join(vcf_fpath + '.gz')
tbi_fpath = gzipped_fpath + '.tbi'
if cnf.reuse_intermediate and \
file_exists(gzipped_fpath) and \
file_exists(tbi_fpath) and getctime(tbi_fpath) >= getctime(gzipped_fpath):
info('Actual compressed VCF and index exist, reusing')
return gzipped_fpath
info('Compressing and tabixing VCF file, writing ' + gzipped_fpath + '(.tbi)')
bgzip = get_system_path(cnf, 'bgzip')
tabix = get_system_path(cnf, 'tabix')
if not bgzip:
err('Cannot index VCF because bgzip is not found in PATH or ' + cnf.sys_cnf)
if not tabix:
err('Cannot index VCF because tabix is not found in PATH or ' + cnf.sys_cnf)
if not bgzip and not tabix:
return vcf_fpath
retrying = False
while True:
if isfile(tbi_fpath): os.remove(tbi_fpath)
if isfile(vcf_fpath):
if isfile(gzipped_fpath):
os.remove(gzipped_fpath)
info('BGzipping VCF')
cmdline = '{bgzip} {vcf_fpath}'.format(**locals())
call(cnf, cmdline, None, **kwargs)
else:
if not verify_file(gzipped_fpath):
err('Neither uncompressed ' + vcf_fpath + ' nor ' + gzipped_fpath + ' exist')
return None
info('Tabixing VCF')
cmdline = '{tabix} {tabix_parameters} {gzipped_fpath}'.format(**locals())
exit_on_error = False
if retrying:
exit_on_error = True
kwargs['exit_on_error'] = exit_on_error
call(cnf, cmdline, **kwargs)
if isfile(gzipped_fpath + '.tbi'):
break
if retrying:
critical('Cannot tabix ' + vcf_fpath)
if not isfile(vcf_fpath):
call(cnf, 'gunzip ' + gzipped_fpath, None)
retrying = True
return gzipped_fpath
def test_time(self):
f = open(support.TESTFN, "wb")
try:
f.write(b"foo")
f.close()
f = open(support.TESTFN, "ab")
f.write(b"bar")
f.close()
f = open(support.TESTFN, "rb")
d = f.read()
f.close()
self.assertEqual(d, b"foobar")
self.assert_(
genericpath.getctime(support.TESTFN) <= genericpath.getmtime(
support.TESTFN))
finally:
if not f.closed:
f.close()
os.remove(support.TESTFN)
def test_time(self):
f = open(support.TESTFN, "wb")
try:
f.write(b"foo")
f.close()
f = open(support.TESTFN, "ab")
f.write(b"bar")
f.close()
f = open(support.TESTFN, "rb")
d = f.read()
f.close()
self.assertEqual(d, b"foobar")
self.assertLessEqual(
genericpath.getctime(support.TESTFN),
genericpath.getmtime(support.TESTFN)
)
finally:
if not f.closed:
f.close()
os.remove(support.TESTFN)
def update_event(self, inp=-1):
self.set_output_val(0, genericpath.getctime(self.input(0)))
@author: VTX
"""
import os
import operator
from genericpath import getctime
rootDir = r"E:\pyTest"
os.chdir(rootDir)
dirs = os.listdir(rootDir)
for i in dirs:
os.chdir(os.path.join(rootDir, i))
subs = os.listdir(os.getcwd())
# print subs
fileList = []
for f in subs:
creaTime = getctime(f)
obj = {"name":f, "creaTime":creaTime}
fileList.append(obj)
fileList.sort(key=operator.itemgetter('creaTime'))
print fileList
ind = 0
for fn in fileList:
os.rename(fn['name'], str(ind) + os.path.splitext(fn['name'])[1])
ind += 1
