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