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How to use compare_files method in toolium
Best Python code snippet using toolium_python
xml_compare_test.py
Source:xml_compare_test.py 
...35 doc_1 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo><bar /></foo>'36 doc_2 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo><bar /></foo>'37 f1 = file_obj_from_string(doc_1)38 f2 = file_obj_from_string(doc_2)39 self.assertIsNone(xml_compare.compare_files(f1, f2))40 def test_doctype_version_mismatch(self):41 # Basic document42 doc_1 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo><bar /></foo>'43 doc_2 = get_xml_declaration('1.1', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo><bar /></foo>'44 f1 = file_obj_from_string(doc_1)45 f2 = file_obj_from_string(doc_2)46 self.assertRaises(Exception, xml_compare.compare_files, (f1, f2))47 def test_doctype_encoding_mismatch(self):48 # Basic document49 doc_1 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo><bar /></foo>'50 doc_2 = get_xml_declaration('1.0', 'utf-16') + (get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo><bar /></foo>').encode('utf-16')51 f1 = file_obj_from_string(doc_1)52 f2 = file_obj_from_string(doc_2)53 self.assertRaises(Exception, xml_compare.compare_files, (f1, f2))54 def test_doctype_system_url_mismatch(self):55 # Basic document56 doc_1 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test1.dtd') + '<foo><bar /></foo>'57 doc_2 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test2.dtd') + '<foo><bar /></foo>'58 f1 = file_obj_from_string(doc_1)59 f2 = file_obj_from_string(doc_2)60 self.assertRaises(Exception, xml_compare.compare_files, (f1, f2))61 def test_doctype_root_tag_mismatch(self):62 # Basic document63 doc_1 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo><bar /></foo>'64 doc_2 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('baz', 'SYSTEM', 'test.dtd') + '<baz><bar /></baz>'65 f1 = file_obj_from_string(doc_1)66 f2 = file_obj_from_string(doc_2)67 self.assertRaises(Exception, xml_compare.compare_files, (f1, f2))68 69 def test_successful_comapre_with_param(self):70 # Basic document71 doc_1 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo a="1" b="c"><bar /></foo>'72 doc_2 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo a="1" b="c"><bar /></foo>'73 f1 = file_obj_from_string(doc_1)74 f2 = file_obj_from_string(doc_2)75 self.assertIsNone(xml_compare.compare_files(f1, f2))76 def test_param_mismatch(self):77 # Basic document78 doc_1 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo a="1"><bar /></foo>'79 doc_2 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo b="c"><bar /></foo>'80 f1 = file_obj_from_string(doc_1)81 f2 = file_obj_from_string(doc_2)82 self.assertRaises(Exception, xml_compare.compare_files, (f1, f2))83 def test_child_num_mismatch(self):84 # Basic document85 doc_1 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo><bar /></foo>'86 doc_2 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo><bar /><bar /></foo>'87 f1 = file_obj_from_string(doc_1)88 f2 = file_obj_from_string(doc_2)89 self.assertRaises(Exception, xml_compare.compare_files, (f1, f2))90 91 def test_child_tag_mismatch(self):92 # Basic document93 doc_1 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo><bar /><car /></foo>'94 doc_2 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo><bar /><bar /></foo>'95 f1 = file_obj_from_string(doc_1)96 f2 = file_obj_from_string(doc_2)97 self.assertRaises(Exception, xml_compare.compare_files, (f1, f2))98 99 def test_text_compare(self):100 # Basic document101 doc_1 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo>bar</foo>'102 doc_2 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo>bar</foo>'103 f1 = file_obj_from_string(doc_1)104 f2 = file_obj_from_string(doc_2)105 self.assertIsNone(xml_compare.compare_files(f1, f2))106 107 def test_text_compare_with_whitespace(self):108 """109 Ensure that whitespace is ignored if ignore_whitespace is set to True.110 """111 # Basic document112 doc_1 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo>bar</foo>'113 doc_2 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + """<foo>114 115bar116</foo>"""117 f1 = file_obj_from_string(doc_1)118 f2 = file_obj_from_string(doc_2)119 self.assertIsNone(xml_compare.compare_files(f1, f2))120 121 def test_text_no_ignore_whitespace(self):122 """123 Ensure that whitespace is not ignored if ignore_whitespace is set to false.124 """125 126 # Basic document127 doc_1 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo>bar</foo>'128 doc_2 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + """<foo>129 130bar131</foo>"""132 f1 = file_obj_from_string(doc_1)133 f2 = file_obj_from_string(doc_2)134 with self.assertRaises(Exception):135 xml_compare.compare_files(f1, f2, ignore_whitespace = False)136 def test_ignore_empty(self):137 """138 Ensure that empty tags are ignored if ignore_empty_tags is set to True.139 140 """141 doc_1 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo></foo>'142 doc_2 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo><bar /></foo>'143 f1 = file_obj_from_string(doc_1)144 f2 = file_obj_from_string(doc_2)145 self.assertIsNone(xml_compare.compare_files(f1, f2))146 147 def test_no_ignore_empty(self):148 """149 Ensure that empty tags are not ignored if ignore_empty_tags is set to False.150 """151 doc_1 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo></foo>'152 doc_2 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo><bar /></foo>'153 f1 = file_obj_from_string(doc_1)154 f2 = file_obj_from_string(doc_2)155 with self.assertRaises(Exception):156 xml_compare.compare_files(f1, f2, ignore_empty_tags = False)157 158 def test_custom_compare_function(self):159 def lower_case_compare(s1, s2):160 return s1.lower() == s2.lower()161 162 doc_1 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo a="HeLlO"></foo>'163 doc_2 = get_xml_declaration('1.0', 'utf-8') + get_xml_doctype('foo', 'SYSTEM', 'test.dtd') + '<foo a="hElLo"></foo>'164 f1 = file_obj_from_string(doc_1)165 f2 = file_obj_from_string(doc_2)166 167 with self.assertRaises(Exception):168 # Compare using the default compare function, which should fail169 xml_compare.compare_files(f1, f2)170 171 # Compare using the custom, lower-case compare function172 self.assertIsNone(xml_compare.compare_files(f1, f2, compare_function = lower_case_compare))...
run_eval_all.py
Source:run_eval_all.py
1import argparse2import sys3import numpy as np4np.random.seed(1)5import os, time6import math7import re8import tempfile9from tempfile import mkdtemp10from subprocess import Popen, check_output11import pandas as pd12import gzip13from os.path import splitext, basename, exists, abspath, isfile, getsize14def filesize(filename):15 if os.path.isfile(filename):16 return getsize(filename)17 else:18 return -119def test_sub_finished(filename, keyword):20 while not isfile(filename):21 time.sleep(60)22 while True:23 with open(filename) as f:24 all_lines = f.readlines()25 if len(all_lines) > 0:26 last = all_lines[-1]27 if keyword in last:28 break29 time.sleep(60)30def main(argv=sys.argv):31 parser = argparse.ArgumentParser(description='iVariant v0.01.')32 parser.add_argument("-m", dest='run_mode', default="all",33 help="annotation input")34 parser.add_argument("-i", dest='input', default="",35 help="annotation input")36 args = parser.parse_args()37 old_path = abspath("./")38 env_path = './'39 gpu_path = './'40 eval_path = './'41 if args.input == '':42 fea_input = '%s/input/input.list' % (env_path)43 else:44 fea_input = args.input45 log_file = './tvar.log'46 cmd = 'rm -f %s' % (log_file)47 check_output(cmd, shell=True)48 #49 # if args.run_mode == 'pca' or args.run_mode == 'all':50 # background_list = '/fs0/yangh8/DVAR/input/train.input'51 # cmd1 = 'python TVar_cpu.py -m fea_train -i %s -t 8' % (background_list)52 # print(cmd1)53 # check_output(cmd1, shell=True)54 if args.run_mode == 'fea' or args.run_mode == 'all':55 for line in open(fea_input):56 cmd = 'python TVar_cpu.py -m fea -i %s -t 8' % (line.rstrip())57 # check_output(cmd, shell=True)58 # if args.run_mode == 'cv' or args.run_mode == 'all':59 # cmds = []60 # train_input = './input/train.list'61 # for line in open(train_input):62 # cmd = 'python TVar_cpu.py -m fea -i %s -t 8' % (line.rstrip())63 # check_output(cmd, shell=True)64 # cmd1 = "python TVar_gpu.py -m cv"65 # cmds.append(cmd1)66 # for cmd in cmds:67 # check_output(cmd, shell=True)68 # cmd = 'python TVar_cpu.py -m cv'69 # check_output(cmd, shell=True)70 # print("CV OK!")71 # return72 if args.run_mode == 'train' or args.run_mode == 'all' or args.run_mode == 'train_score':73 cmds = []74 train_input = './input/train.list'75 for line in open(train_input):76 cmd = 'python TVar_cpu.py -m fea -i %s -t 8' % (line.rstrip())77 # check_output(cmd, shell=True)78 cmd1 = "python TVar_gpu.py -m train"79 # check_output(cmd1, shell=True)80 if args.run_mode == 'score' or args.run_mode == 'all' or args.run_mode == 'train_score':81 cmds = []82 for line in open(fea_input):83 cmd = "python TVar_gpu.py -m score -i %s" % (line.rstrip())84 cmds.append(cmd)85 # for cmd in cmds:86 # check_output(cmd, shell=True)87 # if args.run_mode == 'rare' or args.run_mode == 'all' or args.run_mode == 'train_score':88 # clinvar_input = './input/rare.input'89 # for line in open(clinvar_input):90 # cmd = 'python TVar_cpu.py -m fea -i %s -t 8' % (line.rstrip())91 # #check_output(cmd, shell=True)92 # cmds = []93 # for line in open(clinvar_input):94 # tissue = basename(line.rstrip()).replace("_rare_neg.gz", "")95 # tissue = tissue.replace("_rare_pos.gz", "")96 # cmd = "python TVar_gpu.py -m rare -n %s -i %s" % (tissue, line.rstrip())97 # cmds.append(cmd)98 # for cmd in cmds:99 # check_output(cmd, shell=True)100 # compare_files = []101 # cmd = "rm -f ./eval/rare.log"102 # check_output(cmd, shell=True)103 # for line in open(clinvar_input):104 # base_file = splitext(basename(line.rstrip()))[0]105 # score_file = './score/' + base_file + '.tvar'106 # compare_files.append(score_file)107 # if len(compare_files) == 2:108 # cmd = 'Rscript TVAR_gwas_test.R -p %s -q %s >> ./eval/rare.log' % (compare_files[0], compare_files[1])109 # check_output(cmd, shell=True)110 # compare_files.clear()111 #112 # if args.run_mode == 'gwas' or args.run_mode == 'all' or args.run_mode == 'train_score':113 # clinvar_input = './input/gwas.input'114 # for line in open(clinvar_input):115 # cmd = 'python TVar_cpu.py -m fea -i %s -t 8' % (line.rstrip())116 # #check_output(cmd, shell=True)117 # cmds = []118 # for line in open(clinvar_input):119 # tissue = basename(line.rstrip()).replace("_gwas_neg.gz", "")120 # tissue = tissue.replace("_gwas_pos.gz", "")121 # cmd = "python TVar_gpu.py -m gwas -n %s -i %s" % (tissue, line.rstrip())122 # cmds.append(cmd)123 # for cmd in cmds:124 # check_output(cmd, shell=True)125 # compare_files = []126 # cmd = ''127 # check_output(cmd, shell=True)128 # cmd = "rm -f ./eval/gwas.log"129 # check_output(cmd, shell=True)130 # for line in open(clinvar_input):131 # base_file = splitext(basename(line.rstrip()))[0]132 # score_file = './score/' + base_file + '.tvar'133 # compare_files.append(score_file)134 # if len(compare_files) == 2:135 # cmd = 'Rscript TVAR_gwas_test.R -p %s -q %s >> ./eval/gwas.log' % (compare_files[0], compare_files[1])136 # check_output(cmd, shell=True)137 # compare_files.clear()138 # if args.run_mode == 'eval' or args.run_mode == 'all' or args.run_mode == 'merge':139 # cmd = 'python remove_set.py'140 # check_output(cmd, shell=True)141 # cmd0 = 'python compare.py -m eval > four_sets.log'142 # check_output(cmd0, shell=True)143 if args.run_mode == 'comp' or args.run_mode == 'all' or args.run_mode == 'train_score':144 clinvar_input = './input/rare.input'145 compare_files = []146 log_file = './eval/rare.log'147 cmd = 'rm -f %s' % (log_file)148 check_output(cmd, shell=True)149 for line in open(clinvar_input):150 base_file = splitext(basename(line.rstrip()))[0]151 score_file = './score/' + base_file + '.deepsea'152 compare_files.append(score_file)153 if len(compare_files) == 2:154 cmd = 'Rscript TVAR_gwas_test.R -p %s -q %s >> %s' % (compare_files[0], compare_files[1], log_file)155 check_output(cmd, shell=True)156 compare_files.clear()157if __name__ == "__main__":...
test_filesys.py
Source:test_filesys.py
...33 - Test two text files and verify the contents are different.34 """35 f1 = os.path.join(self._DIR_RESRC, 'test_filesys__file1__diff1.txt')36 f2 = os.path.join(self._DIR_RESRC, 'test_filesys__file2__diff1.txt')37 test = filesys.compare_files(file1=f1, file2=f2)38 utilities.assert_true(expected=False, test=test, msg=self._MSG1)39 def test01__compare_files__diff2(self):40 """Test the ``compare_files`` method, for different files.41 :Test:42 - Test two text files and verify the contents are different,43 although the file signatures are the same.44 """45 f1 = os.path.join(self._DIR_RESRC, 'test_filesys__file1__diff2.txt')46 f2 = os.path.join(self._DIR_RESRC, 'test_filesys__file2__diff2.txt')47 test = filesys.compare_files(file1=f1, file2=f2)48 utilities.assert_true(expected=False, test=test, msg=self._MSG1)49 def test01__compare_files__file_dir(self):50 """Test the ``compare_files`` method, for a file and a directory.51 :Test:52 - Pass a file and a directory into the testing method and verify53 the regular file signature test returns False.54 """55 f1 = os.path.join(self._DIR_RESRC, 'test_filesys__file1__same.txt')56 f2 = self._DIR_RESRC57 test = filesys.compare_files(file1=f1, file2=f2)58 utilities.assert_true(expected=False, test=test, msg=self._MSG1)59 def test01__compare_files__line_endings(self):60 """Test the ``compare_files`` method, for the same file with different61 line engines.62 :Test:63 - Test two text files and verify the contents are same, although64 having different line endings.65 """66 f1 = os.path.join(self._DIR_RESRC, 'test_filesys__file1__dos.txt')67 f2 = os.path.join(self._DIR_RESRC, 'test_filesys__file2__unix.txt')68 test = filesys.compare_files(file1=f1, file2=f2, contents_only=True)69 utilities.assert_true(expected=True, test=test, msg=self._MSG1)70 def test01__compare_files__same(self):71 """Test the ``compare_files`` method, for the same files.72 :Test:73 - Test two text files and verify the contents are the same.74 """75 f1 = os.path.join(self._DIR_RESRC, 'test_filesys__file1__same.txt')76 f2 = os.path.join(self._DIR_RESRC, 'test_filesys__file2__same.txt')77 test = filesys.compare_files(file1=f1, file2=f2)78 utilities.assert_true(expected=True, test=test, msg=self._MSG1)79 def test01__compare_files__sig_only__true(self):80 """Test the ``compare_files`` method, testing the signature only, for81 a True result.82 :Test:83 - Test the signature only for two files, expecting a True response.84 """85 f1 = os.path.join(self._DIR_RESRC, 'test_filesys__file1__same.txt')86 f2 = os.path.join(self._DIR_RESRC, 'test_filesys__file2__same.txt')87 test = filesys.compare_files(file1=f1, file2=f2, sig_only=True)88 utilities.assert_true(expected=True, test=test, msg=self._MSG1)89 def test01__compare_files__sig_only__false(self):90 """Test the ``compare_files`` method, testing the signature only, for91 a False result.92 :Test:93 - Test the signature only for two files, expecting a False response.94 """95 f1 = os.path.join(self._DIR_RESRC, 'test_filesys__file1__diff1.txt')96 f2 = os.path.join(self._DIR_RESRC, 'test_filesys__file2__diff1.txt')97 test = filesys.compare_files(file1=f1, file2=f2, sig_only=True)98 utilities.assert_true(expected=False, test=test, msg=self._MSG1)99 def test02__sig(self):100 """Test the ``_sig`` method, to verify the returned file signature.101 :Test:102 - Test a series of files, and verify the returned signatures are103 as expected.104 """105 f1 = os.path.join(self._DIR_RESRC, 'test_filesys__file1__same.txt')106 f2 = os.path.join(self._DIR_RESRC, 'test_filesys__file1__diff1.txt')107 f3 = os.path.join(self._DIR_RESRC, 'test_filesys__file1__dos.txt')108 files = [f1, f2, f3]109 exp = ((734, 32768, 33204), (734, 32768, 33204), (744, 32768, 33204))110 for f, e in zip(files, exp):111 with self.subTest(msg=f'{f=} {e=}'):...
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