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How to use check_file_exists method in avocado

Best Python code snippet using avocado_python

main.py

Source:main.py

...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,...

test_fileOps.py

Source:test_fileOps.py

...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()...

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