How to use check_file_exists method in avocado

Best Python code snippet using avocado_python

main.py

Source:main.py Github

copy

Full Screen

...36 self.logger = logging.getLogger('timestamp')37 def blast(self, options):38 """Infer gene tree using BLAST."""39 40 check_file_exists(options.query_proteins)41 check_file_exists(options.db_file)42 check_file_exists(options.taxonomy_file)43 44 # sanity check arguments45 if options.prot_model == 'AUTO' and options.tree_program != 'raxml':46 self.logger.error("The 'AUTO' protein model can only be used with RAxML.")47 sys.exit(-1)48 blast_workflow = BlastWorkflow(options.cpus)49 blast_workflow.run(options.query_proteins,50 options.db_file,51 options.custom_db_file,52 options.taxonomy_file,53 options.custom_taxonomy_file,54 options.evalue,55 options.per_identity,56 options.per_aln_len,57 options.max_matches,58 options.homology_search,59 options.min_per_taxa,60 options.consensus,61 options.min_per_bp,62 options.use_trimAl,63 options.restrict_taxon,64 options.msa_program,65 options.tree_program,66 options.prot_model,67 options.skip_rooting,68 options.output_dir)69 70 def concat(self, options):71 """Infer concatenated gene tree."""72 73 make_sure_path_exists(options.output_dir)74 75 c = Concatenate(options.cpus)76 c.run(options.gene_dirs,77 options.min_per_gene,78 options.min_per_bps,79 options.tree_program,80 options.prot_model,81 options.split_chars,82 options.output_dir)83 84 def reduce(self, options):85 """Infer tree for reduced set of genes."""86 87 check_file_exists(options.homolog_file)88 check_file_exists(options.gene_ids)89 check_file_exists(options.taxonomy_file)90 91 make_sure_path_exists(options.output_dir)92 93 r = Reduce(options.cpus)94 r.run(options.homolog_file, 95 options.gene_ids, 96 options.taxonomy_file,97 options.min_per_taxa,98 options.consensus,99 options.min_per_bp,100 options.use_trimAl,101 options.msa_program,102 options.tree_program,103 options.prot_model,104 options.output_dir)105 106 def bootstrap(self, options):107 """Calculate bootstrap support for tree."""108 109 check_file_exists(options.tree)110 111 bootstrap = Bootstrap(options.cpus)112 bootstrap.run(options.tree, 113 options.msa_file,114 options.tree_program,115 options.prot_model,116 options.num_replicates,117 options.output_dir)118 119 def prune(self, options):120 """Prune tree."""121 122 check_file_exists(options.tree)123 check_file_exists(options.taxa_to_retain)124 125 prune = Prune()126 prune.run(options.tree,127 options.taxa_to_retain,128 options.output_tree)129 130 def prokka(self, options):131 """Run Prokka across multiple genome bins."""132 133 prokka = Prokka(options.cpus)134 prokka.run(options.genome_dir, 135 options.kingdom, 136 options.extension, 137 options.output_dir)138 139 def create_db(self, options): 140 """Create dereplicated GeneTreeTk-compatible database."""141 142 create_db = CreateDatabase(options.cpus)143 create_db.run(options.taxonomy,144 options.type_strains,145 options.genome_prot_dir,146 options.extension,147 options.max_taxa,148 options.rank,149 options.per_identity,150 options.per_aln_len,151 options.genomes_to_process,152 options.keep_all_genes,153 options.no_reformat_gene_ids,154 options.output_dir)155 def create_arb_db(self, options):156 ArbDbCreator().create_from_protein_alignment(157 alignment_file=options.alignment_file,158 taxonomy_file=options.taxonomy_file,159 output_file=options.output_file)160 161 def robinson_foulds(self, options):162 """Compare unrooted trees using common statistics."""163 164 check_file_exists(options.tree1)165 check_file_exists(options.tree2)166 167 tc = TreeCompare()168 if options.weighted:169 wrf = tc.weighted_robinson_foulds(options.tree1, 170 options.tree2,171 options.taxa_list)172 print(('Weighted Robinson-Foulds: %.3f' % wrf))173 else:174 rf, normalized_rf = tc.robinson_foulds(options.tree1, 175 options.tree2,176 options.taxa_list)177 print(('Robinson-Foulds: %d' % rf))178 print(('Normalized Robinson-Foulds: %.3f' % normalized_rf))179 180 def supported_splits(self, options):181 """Supported bipartitions of common taxa shared between two trees."""182 183 check_file_exists(options.tree1)184 check_file_exists(options.tree2)185 186 tc = TreeCompare()187 tc.supported_splits(options.tree1, 188 options.tree2,189 options.split_file,190 options.min_support,191 options.max_depth,192 options.taxa_list)193 194 def missing_splits(self, options):195 """Report supported bipartitions in reference tree not in comparison tree."""196 197 check_file_exists(options.ref_tree)198 check_file_exists(options.compare_tree)199 200 tc = TreeCompare()201 tc.report_missing_splits(options.ref_tree, 202 options.compare_tree,203 options.min_support,204 options.taxa_list)205 206 def midpoint(self, options):207 """"Midpoint root tree."""208 209 check_file_exists(options.in_tree)210 211 tree = dendropy.Tree.get_from_path(options.in_tree, 212 schema='newick', rooting='force-rooted', 213 preserve_underscores=True)214 tree.reroot_at_midpoint()215 216 tree.write_to_path(options.out_tree, 217 schema='newick', 218 suppress_rooting=True, 219 unquoted_underscores=True)220 def orthologue(self, options):221 """Infer gene tree using BLAST after Orthologue clustering."""222 223 check_file_exists(options.query_proteins)224 check_file_exists(options.db_file)225 check_file_exists(options.taxonomy_file)226 # sanity check arguments227 if options.prot_model == 'AUTO' and options.tree_program != 'raxml':228 self.logger.error("The 'AUTO' protein model can only be used with RAxML.")229 sys.exit(-1)230 workflow = OrthologueWorkflow(options.cpus)231 workflow.run(232 query_proteins=options.query_proteins,233 db_file=options.db_file,234 #custom_db_file=options.custom_db_file,235 taxonomy_file=options.taxonomy_file,236 #custom_taxonomy_file=options.custom_taxonomy_file,237 evalue=options.evalue,238 per_identity=options.per_identity,239 per_aln_len=options.per_aln_len,...

Full Screen

Full Screen

test_fileOps.py

Source:test_fileOps.py Github

copy

Full Screen

...11 @patch('file_check.FileOps.create_file', return_value=False)12 def test_create_file_dir_fail(self, create_file, check_dir_exists, check_file_exists):13 self.assertEqual(create_file(), False)14 self.assertEqual(check_dir_exists(), True)15 self.assertEqual(check_file_exists(), True)16 @patch('file_check.FileOps.check_file_exists', return_value=True)17 @patch('file_check.FileOps.check_dir_exists', return_value=False)18 @patch('file_check.FileOps.create_file', return_value=True)19 def test_create_file_dir_fail_2(self, create_file, check_dir_exists, check_file_exists):20 self.fops.create_file()21 self.fops.check_dir_exists()22 self.fops.check_file_exists()23 assert create_file.called24 check_dir_exists.assert_called_with()...

Full Screen

Full Screen

Automation Testing Tutorials

Learn to execute automation testing from scratch with LambdaTest Learning Hub. Right from setting up the prerequisites to run your first automation test, to following best practices and diving deeper into advanced test scenarios. LambdaTest Learning Hubs compile a list of step-by-step guides to help you be proficient with different test automation frameworks i.e. Selenium, Cypress, TestNG etc.

LambdaTest Learning Hubs:

YouTube

You could also refer to video tutorials over LambdaTest YouTube channel to get step by step demonstration from industry experts.

Run avocado automation tests on LambdaTest cloud grid

Perform automation testing on 3000+ real desktop and mobile devices online.

Try LambdaTest Now !!

Get 100 minutes of automation test minutes FREE!!

Next-Gen App & Browser Testing Cloud

Was this article helpful?

Helpful

NotHelpful