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How to use annotate method in autotest

Best Python code snippet using autotest_python

annotate.py

Source:annotate.py

1import shutil2import sys3from genomad import database, mmseqs2, prodigal, sequence, taxonomy, utils4from genomad._paths import GenomadOutputs5def write_genes_output(genes_output, database_obj, prodigal_obj, mmseqs2_obj):6    marker_annotation_dict = database_obj.get_marker_annotation()7    gene_match_dict = mmseqs2_obj.get_matches()8    taxdb = database_obj.get_taxdb()9    with open(genes_output, "w") as fout:10        fout.write(11            "gene\tstart\tend\tlength\tstrand\tgc_content\tgenetic_code\trbs_motif\t"12            "marker\tevalue\tbitscore\tuscg\tplasmid_hallmark\tvirus_hallmark\ttaxid\t"13            "taxname\tannotation_conjscan\tannotation_accessions\tannotation_description\n"14        )15        for (16            contig,17            gene_num,18            start,19            end,20            strand,21            rbs,22            code,23            gc,24        ) in prodigal_obj.proteins():25            gene = f"{contig}_{gene_num}"26            match, evalue, bitscore, taxid = gene_match_dict.get(27                gene, ("NA", "NA", "NA", 1)28            )29            taxname = taxdb.taxid2name[taxid] if taxid != 1 else "NA"30            (31                uscg,32                plasmid_hallmark,33                virus_hallmark,34                conjscan,35                accession,36                description,37            ) = marker_annotation_dict.get(match, (0, 0, 0, "NA", "NA", "NA"))38            gene_length = end - start + 139            fout.write(40                f"{gene}\t{start}\t{end}\t{gene_length}\t{strand}\t{gc:.3f}\t{code}\t"41                f"{rbs}\t{match}\t{evalue}\t{bitscore}\t{uscg}\t{plasmid_hallmark}\t"42                f"{virus_hallmark}\t{taxid}\t{taxname}\t{conjscan}\t{accession}\t{description}\n"43            )44def main(45    input_path,46    output_path,47    database_path,48    use_minimal_db,49    restart,50    threads,51    verbose,52    sensitivity,53    evalue,54    splits,55    cleanup,56):57    # Create `output_path` if it does not exist58    if not output_path.is_dir():59        output_path.mkdir()60    # Define the prefix and the output files61    prefix = input_path.stem62    if utils.is_compressed(input_path) != utils.Compression.uncompressed:63        prefix = prefix.rsplit(".", 1)[0]64    outputs = GenomadOutputs(prefix, output_path)65    # Create the console66    console = utils.HybridConsole(output_file=outputs.annotate_log, verbose=verbose)67    # Create a dictionary containing the parameters68    parameter_dict = {69        "use_minimal_db": use_minimal_db,70        "sensitivity": sensitivity,71        "evalue": evalue,72    }73    # Display the module header74    utils.display_header(75        console,76        "annotate",77        (78            "This will perform gene calling in the input sequences and "79            "annotate the predicted proteins with geNomad's markers."80        ),81        outputs.annotate_dir,82        [83            outputs.annotate_execution_info,84            outputs.annotate_genes_output,85            outputs.annotate_taxonomy_output,86            outputs.annotate_mmseqs2_output,87            outputs.annotate_proteins_output,88        ],89        [90            "execution parameters",91            "gene annotation data",92            "taxonomic assignment",93            "MMseqs2 output file",94            "protein FASTA file",95        ],96    )97    # Check if the required binaries are in the PATH98    required_executables = ["mmseqs", "prodigal-gv"]99    if missing_executables := utils.check_executables(required_executables):100        console.error(101            "These dependencies are missing and need to be installed: [u]"102            + "[/u], [u]".join(missing_executables)103            + "[/u]. The current execution will be terminated."104        )105        sys.exit(1)106    # Check the input FASTA file107    if not sequence.check_fasta(input_path):108        console.error(109            f"[u]{input_path}[/u] is either empty or contains multiple entries "110            "with the same identifier. Please check your input FASTA file and "111            "execute [cyan]genomad annotate[/cyan] again."112        )113        sys.exit(1)114    # Print initial log115    console.log("Executing [cyan]genomad annotate[/cyan].")116    # Check if steps can be skipped117    skip = False118    if (119        outputs.annotate_execution_info.exists()120        and any(121            [122                outputs.annotate_proteins_output.exists(),123                outputs.annotate_genes_output.exists(),124            ]125        )126        and not restart127    ):128        # Check if the previous execution used the same input file and parameters129        if utils.compare_executions(130            input_path, parameter_dict, outputs.annotate_execution_info131        ):132            skip = True133            console.log(134                "Previous execution detected. Steps will be skipped "135                "unless their outputs are not found. Use the [cyan]"136                "--restart[/cyan] option to force the execution of all "137                "the steps again."138            )139        else:140            console.log(141                "The input file or the parameters changed since the last "142                "execution. Previous outputs will be overwritten."143            )144    # If necessary, create the subdirectory145    if not outputs.annotate_dir.is_dir():146        console.log(f"Creating the [green]{outputs.annotate_dir}[/green] directory.")147        outputs.annotate_dir.mkdir()148    # Write the execution data to `execution_info_output`149    utils.write_execution_info(150        "annotate", input_path, parameter_dict, outputs.annotate_execution_info151    )152    # Initialize the database object153    database_obj = database.Database(database_path)154    # Run prodigal-gv155    prodigal_obj = prodigal.Prodigal(input_path, outputs.annotate_proteins_output)156    if skip and outputs.annotate_proteins_output.exists():157        console.log(158            f"[green]{outputs.annotate_proteins_output.name}[/green] was found. "159            "Skipping gene prediction with prodigal-gv."160        )161    else:162        with console.status("Predicting proteins with prodigal-gv."):163            prodigal_obj.run_parallel_prodigal(threads)164            console.log(165                "Proteins predicted with prodigal-gv were written to "166                f"[green]{outputs.annotate_proteins_output.name}[/green]."167            )168    # Run MMseqs2169    mmseqs2_obj = mmseqs2.MMseqs2(170        outputs.annotate_mmseqs2_output,171        outputs.annotate_mmseqs2_dir,172        outputs.annotate_proteins_output,173        database_obj,174        use_minimal_db=use_minimal_db,175    )176    if skip and outputs.annotate_mmseqs2_output.exists():177        console.log(178            f"[green]{outputs.annotate_mmseqs2_output.name}[/green] was found. "179            "Skipping protein annotation with MMseqs2."180        )181    else:182        with console.status(183            "Annotating proteins with MMseqs2 and geNomad database "184            f"(v{database_obj.version})."185        ):186            mmseqs2_obj.run_mmseqs2(threads, sensitivity, evalue, splits)187            console.log(188                "Proteins annotated with MMseqs2 and geNomad database "189                f"(v{database_obj.version}) were written to "190                f"[green]{outputs.annotate_mmseqs2_output.name}[/green]."191            )192    if cleanup and outputs.annotate_mmseqs2_dir.is_dir():193        console.log(f"Deleting [green]{outputs.annotate_mmseqs2_dir.name}[/green].")194        shutil.rmtree(outputs.annotate_mmseqs2_dir)195    # Write `annotate_genes_output`196    with console.status(197        f"Writing [green]{outputs.annotate_genes_output.name}[/green]."198    ):199        write_genes_output(200            outputs.annotate_genes_output, database_obj, prodigal_obj, mmseqs2_obj201        )202        console.log(203            f"Gene data was written to [green]{outputs.annotate_genes_output.name}[/green]."204        )205    # Write `annotate_taxonomy_output`206    with console.status(207        f"Writing [green]{outputs.annotate_taxonomy_output.name}[/green]."208    ):209        taxonomy.write_taxonomic_assignment(210            outputs.annotate_taxonomy_output,211            outputs.annotate_genes_output,212            database_obj,213        )214        console.log(215            f"Taxonomic assignment data was written to [green]{outputs.annotate_taxonomy_output.name}[/green]."216        )...

minesweeper_test.py

Source:minesweeper_test.py

2from minesweeper import annotate3# Tests adapted from `problem-specifications//canonical-data.json`4class MinesweeperTest(unittest.TestCase):5    def test_no_rows(self):6        self.assertEqual(annotate([]), [])7    def test_no_columns(self):8        self.assertEqual(annotate([""]), [""])9    def test_no_mines(self):10        self.assertEqual(annotate(["   ", "   ", "   "]), ["   ", "   ", "   "])11    def test_minefield_with_only_mines(self):12        self.assertEqual(annotate(["***", "***", "***"]), ["***", "***", "***"])13    def test_mine_surrounded_by_spaces(self):14        self.assertEqual(annotate(["   ", " * ", "   "]), ["111", "1*1", "111"])15    def test_space_surrounded_by_mines(self):16        self.assertEqual(annotate(["***", "* *", "***"]), ["***", "*8*", "***"])17    def test_horizontal_line(self):18        self.assertEqual(annotate([" * * "]), ["1*2*1"])19    def test_horizontal_line_mines_at_edges(self):20        self.assertEqual(annotate(["*   *"]), ["*1 1*"])21    def test_vertical_line(self):22        self.assertEqual(annotate([" ", "*", " ", "*", " "]), ["1", "*", "2", "*", "1"])23    def test_vertical_line_mines_at_edges(self):24        self.assertEqual(annotate(["*", " ", " ", " ", "*"]), ["*", "1", " ", "1", "*"])25    def test_cross(self):26        self.assertEqual(27            annotate(["  *  ", "  *  ", "*****", "  *  ", "  *  "]),28            [" 2*2 ", "25*52", "*****", "25*52", " 2*2 "],29        )30    def test_large_minefield(self):31        self.assertEqual(32            annotate([" *  * ", "  *   ", "    * ", "   * *", " *  * ", "      "]),33            ["1*22*1", "12*322", " 123*2", "112*4*", "1*22*2", "111111"],34        )35    # Additional tests for this track36    def test_annotate_9(self):37        self.assertEqual(38            annotate(["     ", "   * ", "     ", "     ", " *   "]),39            ["  111", "  1*1", "  111", "111  ", "1*1  "],40        )41    def test_different_len(self):42        with self.assertRaisesWithMessage(ValueError):43            annotate([" ", "*  ", "  "])44    def test_invalid_char(self):45        with self.assertRaisesWithMessage(ValueError):46            annotate(["X  * "])47    # Utility functions48    def assertRaisesWithMessage(self, exception):49        return self.assertRaisesRegex(exception, r".+")50if __name__ == "__main__":...

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