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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,153 @@ | ||
| import logging | ||
| import shutil | ||
| import sys | ||
| from pathlib import Path | ||
|
|
||
| import rich | ||
| import rich.console | ||
| import rich.traceback | ||
| import rich_click as click | ||
| from rich.logging import RichHandler | ||
|
|
||
| import bactopia | ||
|
|
||
| # Set up Rich | ||
| stderr = rich.console.Console(stderr=True) | ||
| rich.traceback.install(console=stderr, width=200, word_wrap=True, extra_lines=1) | ||
| click.rich_click.USE_RICH_MARKUP = True | ||
| click.rich_click.OPTION_GROUPS = { | ||
| "bactopia-atb-formatter": [ | ||
| {"name": "Required Options", "options": ["--path"]}, | ||
| { | ||
| "name": "Bactopia Directory Structure Options", | ||
| "options": [ | ||
| "--bactopia-dir", | ||
| "--publish-mode", | ||
| "--recursive", | ||
| ], | ||
| }, | ||
| { | ||
| "name": "Additional Options", | ||
| "options": [ | ||
| "--verbose", | ||
| "--silent", | ||
| "--version", | ||
| "--help", | ||
| ], | ||
| }, | ||
| ] | ||
| } | ||
|
|
||
|
|
||
| def search_path(path, pattern, recursive=False): | ||
| if recursive: | ||
| return Path(path).rglob(pattern) | ||
| else: | ||
| return Path(path).glob(pattern) | ||
|
|
||
|
|
||
| def create_sample_directory(sample, assembly, bactopia_dir, publish_mode="symlink"): | ||
| logging.debug(f"Creating {sample} directory ({bactopia_dir}/{sample})") | ||
| sample_dir = Path(f"{bactopia_dir}/{sample}") | ||
| if not sample_dir.exists(): | ||
| sample_dir.mkdir(parents=True, exist_ok=True) | ||
|
|
||
| # Make remaining subdirectories (which will be empty) | ||
| Path(f"{bactopia_dir}/{sample}/main").mkdir(parents=True, exist_ok=True) | ||
| Path(f"{bactopia_dir}/{sample}/main/gather").mkdir(parents=True, exist_ok=True) | ||
| Path(f"{bactopia_dir}/{sample}/main/assembler").mkdir(parents=True, exist_ok=True) | ||
|
|
||
| # Write the meta.tsv file | ||
| logging.debug(f"Writing {sample}-meta.tsv") | ||
| with open(f"{bactopia_dir}/{sample}/main/gather/{sample}-meta.tsv", "w") as meta_fh: | ||
| meta_fh.write( | ||
| "sample\truntype\toriginal_runtype\tis_paired\tis_compressed\tspecies\tgenome_size\n" | ||
| ) | ||
| meta_fh.write( | ||
| f"{sample}\tassembly_accession\tassembly_accession\tfalse\tfalse\null\0\n" | ||
| ) | ||
|
|
||
| # Write the assembly file | ||
| final_assembly = f"{bactopia_dir}/{sample}/main/assembler/{sample}.fna" | ||
| final_assembly_path = Path(final_assembly) | ||
| if publish_mode == "symlink": | ||
| logging.debug(f"Creating symlink of {assembly} at {final_assembly}") | ||
| final_assembly_path.symlink_to(assembly) | ||
| else: | ||
| logging.debug(f"Copying {assembly} to {final_assembly}") | ||
| shutil.copyfile(assembly, final_assembly) | ||
|
|
||
| return True | ||
|
|
||
|
|
||
| @click.command() | ||
| @click.version_option(bactopia.__version__, "--version", "-V") | ||
| @click.option( | ||
| "--path", "-p", required=True, help="Directory where FASTQ files are stored" | ||
| ) | ||
| @click.option( | ||
| "--bactopia-dir", | ||
| "-b", | ||
| default="bactopia", | ||
| show_default=True, | ||
| help="The path you would like to place bactopia structure", | ||
| ) | ||
| @click.option( | ||
| "--publish-mode", | ||
| "-m", | ||
| default="symlink", | ||
| show_default=True, | ||
| type=click.Choice(["symlink", "copy"], case_sensitive=False), | ||
| help="Designates plascement of assemblies will be handled", | ||
| ) | ||
| @click.option( | ||
| "--recursive", "-r", is_flag=True, help="Traverse recursively through provided path" | ||
| ) | ||
| @click.option("--verbose", is_flag=True, help="Increase the verbosity of output") | ||
| @click.option("--silent", is_flag=True, help="Only critical errors will be printed") | ||
| def atb_formatter( | ||
| path, | ||
| bactopia_dir, | ||
| publish_mode, | ||
| recursive, | ||
| verbose, | ||
| silent, | ||
| ): | ||
| """Restructure All-the-Bacteria assemblies to allow usage with Bactopia Tools""" | ||
| # Setup logs | ||
| logging.basicConfig( | ||
| 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)) | ||
| ], | ||
| ) | ||
| logging.getLogger().setLevel( | ||
| logging.ERROR if silent else logging.DEBUG if verbose else logging.INFO | ||
| ) | ||
|
|
||
| abspath = Path(path).absolute() | ||
| fasta_ext = ".fa" | ||
|
|
||
| # Match Assemblies | ||
| count = 0 | ||
| logging.info( | ||
| "Setting up Bactopia directory structure (use --verbose to see more details)" | ||
| ) | ||
| for fasta in search_path(abspath, f"*{fasta_ext}", recursive=recursive): | ||
| fasta_name = fasta.name.replace(fasta_ext, "") | ||
| create_sample_directory(fasta_name, fasta, bactopia_dir, publish_mode) | ||
| count += 1 | ||
| logging.info(f"Bactopia directory structure created at {bactopia_dir}") | ||
| logging.info(f"Total assemblies processed: {count}") | ||
|
|
||
|
|
||
| def main(): | ||
| if len(sys.argv) == 1: | ||
| atb_formatter.main(["--help"]) | ||
| else: | ||
| atb_formatter() | ||
|
|
||
|
|
||
| if __name__ == "__main__": | ||
| main() |
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