diff --git a/CHANGELOG.md b/CHANGELOG.md index c322af5..58ab246 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,7 +2,9 @@ ## 1.4.0 - +- added: + - `bactopia-pubmlst-setup` to setup PubMLST REST API connections + - `bactopia-pubmlst-build` to build PubMLST databases compatible with `mlst` Bactopia Tool ## 1.3.0 diff --git a/README.md b/README.md index 54d3b04..6fa8837 100644 --- a/README.md +++ b/README.md @@ -9,14 +9,18 @@ A Python package for working with [Bactopia](https://bactopia.github.io/) There are many subcommands available in Bactopia. Here is a brief description of each command: -| Command | Description | -|----------------------|----------------------------------------------------------------------------| -| `bactopia-citations` | Print out tools and citations used throughout Bactopia | -| `bactopia-datasets` | Download optional datasets to supplement your analyses with Bactopia | -| `bactopia-download` | Builds Bactopia environments for use with Nextflow. | -| `bactopia-prepare` | Create a 'file of filenames' (FOFN) of samples to be processed by Bactopia | -| `bactopia-search` | Query against ENA and SRA for public accessions to process with Bactopia | -| `bactopia-summary` | Generate a summary table from the Bactopia results. | +| Command | Description | +|---------------------------|----------------------------------------------------------------------------| +| `bactopia-citations` | Print out tools and citations used throughout Bactopia | +| `bactopia-datasets` | Download optional datasets to supplement your analyses with Bactopia | +| `bactopia-download` | Builds Bactopia environments for use with Nextflow. | +| `bactopia-prepare` | Create a 'file of filenames' (FOFN) of samples to be processed by Bactopia | +| `bactopia-search` | Query against ENA and SRA for public accessions to process with Bactopia | +| `bactopia-summary` | Generate a summary table from the Bactopia results. | +| `bactopia-atb-downloader` | Download assemblies from AllTheBacteria for use with Bactopia Tools | +| `bactopia-atb-formatter` | Restructure All-the-Bacteria assemblies to allow usage with Bactopia Tools | +| `bactopia-pubmlst-setup` | One-time setup for interacting with the PubMLST API | +| `bactopia-pubmlst-build` | Build PubMLST databases for use with the 'mlst' Bactopia Tool. | Below is the `--help` output for each subcommand. diff --git a/bactopia/cli/pubmlst/build.py b/bactopia/cli/pubmlst/build.py index 14b9b85..ec2caed 100644 --- a/bactopia/cli/pubmlst/build.py +++ b/bactopia/cli/pubmlst/build.py @@ -13,6 +13,7 @@ available_databases, build_blast_db, download_database, + print_citation, ) # Set up Rich @@ -21,7 +22,7 @@ click.rich_click.USE_RICH_MARKUP = True click.rich_click.OPTION_GROUPS = { # Use underscores in parameters, since these are also passed to Nextflow - "bactopia-pubmlst-download": [ + "bactopia-pubmlst-build": [ { "name": "Required Options", "options": [ @@ -63,9 +64,7 @@ @click.option( "--database", "-d", - default="pubmlst_yersinia_seqdef", - show_default=True, - help="The organism database to interact with for setup. (Use 'all' to download all databases.)", + help="A known organism database to download. (Use 'all' to download all databases.)", ) @click.option( "--site", @@ -78,7 +77,7 @@ @click.option( "--token-dir", "-t", - default=".bactopia/pubmlst", + default=f"{Path.home()}/.bactopia", show_default=True, help="The directory where the token file is saved.", ) @@ -114,7 +113,7 @@ def pubmlst_download( verbose: bool, silent: bool, ): - """Download specific database files from PubMLST or Pasteur.""" + """Build PubMLST databases for use with the 'mlst' Bactopia Tool.""" # Setup logs logging.basicConfig( format="%(asctime)s:%(name)s:%(levelname)s - %(message)s", @@ -184,9 +183,11 @@ def pubmlst_download( if not skip_blast: # Build MLST database build_blast_db( - f"{out_dir}/mlstdb", + out_dir, ) + print_citation() + def main(): if len(sys.argv) == 1: diff --git a/bactopia/cli/pubmlst/setup.py b/bactopia/cli/pubmlst/setup.py index 29e7cf8..adf4e00 100644 --- a/bactopia/cli/pubmlst/setup.py +++ b/bactopia/cli/pubmlst/setup.py @@ -9,7 +9,7 @@ from rich.logging import RichHandler import bactopia -from bactopia.databases.pubmlst.utils import setup_pubmlst +from bactopia.databases.pubmlst.utils import print_citation, setup_pubmlst # Set up Rich stderr = rich.console.Console(stderr=True) @@ -58,6 +58,7 @@ @click.option( "--site", "-s", + default="pubmlst", show_default=True, type=click.Choice(["pubmlst", "pasteur"], case_sensitive=True), help="Only print citation matching a given name", @@ -72,7 +73,7 @@ @click.option( "--save-dir", "-sd", - default=".bactopia/pubmlst", + default=f"{Path.home()}/.bactopia", show_default=True, help="The directory to save the token", ) @@ -95,7 +96,14 @@ def pubmlst_setup( format="%(asctime)s:%(name)s:%(levelname)s - %(message)s", datefmt="%Y-%m-%d %H:%M:%S", handlers=[ - RichHandler(rich_tracebacks=True, console=rich.console.Console(stderr=True)) + RichHandler( + rich_tracebacks=True, + console=rich.console.Console(stderr=True), + show_time=True if verbose else False, + show_level=True if verbose else False, + show_path=True, + markup=True, + ) ], ) logging.getLogger().setLevel( @@ -114,6 +122,7 @@ def pubmlst_setup( ) sys.exit(1) setup_pubmlst(site, database, token_file, client_id, client_secret) + print_citation() def main(): diff --git a/bactopia/databases/pubmlst/utils.py b/bactopia/databases/pubmlst/utils.py index 2f3cef4..092d51c 100644 --- a/bactopia/databases/pubmlst/utils.py +++ b/bactopia/databases/pubmlst/utils.py @@ -16,6 +16,21 @@ from bactopia.utils import execute +def print_citation(): + """ + Print the citation for PubMLST and Bactopia + """ + logging.info( + "\n\n" + "If you make use of 'bactopia-pubmlst-(setup|build)' commands and 'PubMLST' database files, please cite the following:\n\n" + "'PubMLST'\n" + "Jolley, K. A., Bray, J. E., & Maiden, M. C. J. (2018). Open-access bacterial population genomics: BIGSdb software, the Pubmlst.org website and their applications. Wellcome Open Research, 3, 124. https://doi.org/10.12688/wellcomeopenres.14826.1\n\n" + "'Bactopia'\n" + "Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020) https://doi.org/10.1128/mSystems.00190-20\n\n" + "adios!" + ) + + def setup_pubmlst( site: str, database: str, token_file: str, client_id: str, client_secret: str ): @@ -115,7 +130,7 @@ def check_session(site: str, token_file: str, database: str = "yersinia") -> dic tokens = parse_json(token_file) if not tokens["session_token"] or not tokens["session_secret"]: - logging.warning("Session token not found, will request a new one") + logging.debug("Session token not found, will request a new one") needs_update = True else: # Try querying the API to see if the session token is still valid @@ -548,13 +563,14 @@ def download_database( logging.info(f"'{database}' complete") -def build_blast_db(database_dir: str): +def build_blast_db(out_dir: str): """ Build a BLAST database from the loci FASTA files that is compatible with 'tseemann/mlst' Args: - database_dir (str): The directory containing the loci FASTA files + out_dir (str): The directory containing the loci FASTA files """ + database_dir = f"{out_dir}/mlstdb" blast_db_dir = f"{database_dir}/blast" if not Path(blast_db_dir).exists(): Path(blast_db_dir).mkdir(parents=True, exist_ok=True) @@ -579,7 +595,7 @@ def build_blast_db(database_dir: str): # Build the BLAST database execute( - f"makeblastdb -hash_index -in mlst.fa -dbtype nucl -title 'PubMLST' -parse_seqids", + "makeblastdb -hash_index -in mlst.fa -dbtype nucl -title 'PubMLST' -parse_seqids", directory=blast_db_dir, ) @@ -589,4 +605,5 @@ def build_blast_db(database_dir: str): # Tar the BLAST database logging.info(f"Save BLAST database to '{database_dir}/mlst.tar.gz'") - execute(f"tar -czvf mlst.tar.gz mlstdb/", directory=database_dir) + execute("tar -czvf mlst.tar.gz mlstdb/", directory=out_dir) + shutil.move(f"{out_dir}/mlst.tar.gz", f"{database_dir}/mlst.tar.gz") diff --git a/bactopia/reports/__init__.py b/bactopia/reports/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/bactopia/reports/templates/__init__.py b/bactopia/reports/templates/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/environment.yml b/environment.yml index 9804812..cc623da 100644 --- a/environment.yml +++ b/environment.yml @@ -2,7 +2,8 @@ channels: - conda-forge - bioconda dependencies: + - blast - pigz - - poetry =1.3 - - python >=3.8 + - poetry + - python >=3.8,<3.12 - wget diff --git a/poetry.lock b/poetry.lock index 82c875d..4946679 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,12 +1,12 @@ -# This file is automatically @generated by Poetry and should not be changed by hand. +# This file is automatically @generated by Poetry 2.0.1 and should not be changed by hand. 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