How to use method_fail method in grail

Best Python code snippet using grail_python

00_amrfinder_filter.py

Source:00_amrfinder_filter.py

1#!/usr/bin/env python2'''Filter AMRFinder Plus results for high confidence matches.3This script filters AMRFinder output tables for matches, with4default criteria focused on high quality & complete matches.5e.g. >90% identity, >90% match length.6Script options also allow filtering for just AMR determinants,7or conversely, only non-AMR results (e.g. virulence/stress).8'''9import argparse10def dict_writer(protein_id, sequence_name, HMM_id, 11	method_type, d, line, duplicates):12	if sequence_name in d.values():13		duplicates += 1	14	elif HMM_id in d.values():15		duplicates += 116	else:17		d[protein_id] = line18	return d, duplicates19def method_filter(infile, outfile, method, just_AMR, no_AMR):20	d = {}				# initialize dictionary for writing matches21	d_amr = {}			# initialize dictionary for writing just AMR matches22	d_no_amr = {}		# initialize dictionary for writing just non-AMR matches23	total = 0			# counter for number of AMRFinder lines/matches24	method_match = 0	# counter for number of genes matching method criteria25	method_fail = 0		# counter for number of genes failing method criteria filter26	duplicates = 0		# counter for number of duplicate genes27	just_AMR_count = 028	no_AMR_count = 029	if method == "complete":30		methods = ["ALLELE", "EXACT", "BLAST", "HMM"]31	elif method == "add_partial_end":32		methods = ["ALLELE", "EXACT", "BLAST", "HMM", "PARTIAL_CONTIG_END"]33	with open(infile, 'r') as file:34		for line in file:35			total += 136			X = line.rstrip().split('\t')37			protein_id = X[0]		# protein id (with contig)38			gene_symbol = X[1]		# gene symbol39			sequence_name = X[2] 	# sequence name40			scope = X[3]			# core / plus41			element_type = X[4]		# AMR, STRESS, etc.42			element_subtype = X[5]	# AMR, Metal, Acid, etc.43			amr_class = X[6]		# e.g. glycopeptide, aminoglycoside, etc.44			amr_subclass = X[7]		# e.g. vancomycin, streptomycin, etc.45			method_type = X[8]			# e.g. PARTIALP, HMM, EXACTP, etc.46			target_l = X[9]			# target length47			ref_l = X[10]			# ref length48			cov_pct = X[11]			# coverage percent [breadth]49			pct_ident = X[12]		# percent identity to reference50			align_l = X[13]			# alignment length51			accession = X[14]		# NCBI accession for closest sequence52			ref_name = X[15]		# name of closest sequence53			HMM_id = X[16]			# id of closest HMM54			HMM_desc = X[17]		# description of closest HMM55#			print(line)56			# print(method_type, element_type)57			if method_type.startswith(tuple(methods)):58				# add option to filter just AMR results59				if just_AMR:60					if element_type == 'AMR':61						d_amr, duplicates = dict_writer(protein_id, sequence_name,62							HMM_id, method_type, d_amr, line, duplicates)63						just_AMR_count += 164				if no_AMR:65					if element_type != 'AMR':66						d_no_amr, duplicates = dict_writer(protein_id, sequence_name,67							HMM_id, method_type, d_no_amr, line, duplicates)68						no_AMR_count += 169				d, duplicates = dict_writer(protein_id, sequence_name,70					 HMM_id, method_type, d, line, duplicates)71				method_match += 172			else:73				method_fail += 174	print('Writing output file(s)...')75	with open(f"{outfile}.tsv", 'w') as file:76		for key, value in d.items():77			file.write(value)78	if no_AMR:79		with open(f"{outfile}_noAMR.tsv", 'w') as noAMR_file:80			for key, value in d_no_amr.items():81				noAMR_file.write(value)82	if just_AMR:83		with open(f"{outfile}_justAMR.tsv", 'w') as file:84			for key, value in d_amr.items():85				file.write(value)86			87	print('Done.')88	print('')89	print('Filter statistics:')90	print(' - total hits in unfiltered AMRFinder table: ', total)91	print(' - lines passing filter:', method_match, "(", round((method_match/total * 100), 1), "% ).")92	print(' - lines failing filter:', method_fail, "(", round((method_fail/total * 100), 1), "% ).")93	if just_AMR:94		print(' - just AMR results:', just_AMR_count)95	if no_AMR:96		print(' - non-AMR results:', no_AMR_count)97	print(' - duplicate HMM ids:', duplicates, "(", round((duplicates/total * 100), 1), "% ).")98def main():99	# configure argparse arguments & pass to method_filter100	parser = argparse.ArgumentParser(101		description=__doc__,102		formatter_class = argparse.RawDescriptionHelpFormatter103		)104	parser.add_argument(105		'-i', '--input',106		help = 'Please specify AMRFinder input tsv file name & path.',107		metavar = '',108		type=str,109		required=True110		)111	parser.add_argument(112		'-o', '--output',113		help = 'Please specify AMRFinder filtered prefix & path for output tsv.',114		metavar = '',115		type=str,116		required=True117		)118	parser.add_argument(119		'-m', '--method',120		help = 'Please specify filtered AMRFinder output tsv file name & path.\121		Select from: complete -or- add_partial_end',122		metavar = '',123		type=str,124		default = 'complete',125		choices=['complete', 'add_partial_end']126		)127	parser.add_argument(128		'-j', '--just_AMR',129		help = 'Flag to write tsv with just AMR results',130		required=False,131		action='store_true'132		)133	parser.add_argument(134		'-v', '--virulence_stress',135		help = 'Flag to write tsv without AMR results (e.g. filter only virulence, stress)',136		required=False,137		action='store_true'138		)139	args=vars(parser.parse_args())140	print('')141	print("File:", args['input'])142	print("Method:", args['method'])143	print('Filtering results...')144	method_filter(args['input'], args['output'], 145		args['method'], args['just_AMR'], args['virulence_stress'])146if __name__ == "__main__":...

test_direct_exception_handling.py

Source:test_direct_exception_handling.py

...12    raise failure_exception13@step14def error_step():15    raise error_exception16def method_fail():17    passed_step()18    failed_step()19    raise Exception('we should not reach this')20@step(step_group=True)21def failed_group():22    passed_step()23    failed_step()24    raise Exception('we should not reach this too')25def method_fail_group():26    failed_group()27    raise Exception('we should not reach this even here')28def method_error():29    passed_step()30    error_step()31    raise Exception('we should not reach this')32@step(step_group=True)33def error_group():34    passed_step()35    error_step()36    raise Exception('we should not reach this too')37def method_error_group():38    error_group()39    raise Exception('we should not reach this even here')40class TestDirectHandling(TestCase):41    def test_method_fail(self):42        try:43            validate_method_output(method_fail, 'PASSED passed step\n'44                                                'FAILED failed step')45        except Exception as inst:46            eq_(inst, failure_exception)47    def test_group_fail(self):48        try:49            validate_method_output(method_fail_group, 'FAILED failed group\n'50                                                      '  PASSED passed step\n'51                                                      '  FAILED failed step')52        except Exception as inst:53            eq_(inst, failure_exception)54    def test_method_error(self):55        try:...

conditions.py

Source:conditions.py

...9    def function(arg): # ordinary function10        pass11    class C(object):12        @post_condition(lambda ret: ret > 0)13        def method_fail(self):14            return 015        @post_condition(lambda ret: ret > 0)16        def method_success(self):17            return 118    """19    def decorator(func):20        @functools.wraps(func)  # presever name, docstring, etc21        def wrapper(*args, **kwargs):  # NOTE: no self22            if pre_condition is not None:23                assert pre_condition(*args, **kwargs), "Pre-Condition was not met!"24            retval = func(*args, **kwargs)  # call original function or method25            if post_condition is not None:26                assert post_condition(retval), "Post-Condition was not met!"27            return retval...

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