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import logging
import os
import sys
from typing import List
import click
from ._version import __version__
from .bus_file import create_from_fastq
@click.group()
@click.option('--show-message/--hide-message', default=True)
@click.option('--verbosity', default="info", type=click.Choice(['error', 'warning', 'info', 'debug']))
def cli(show_message: bool = True, verbosity: str = "info") -> None:
level = {"error": 40, "warning": 30, "info": 20, "debug": 10}[verbosity]
logging.basicConfig(stream=sys.stdout, format='%(asctime)s - %(levelname)s - %(message)s', level=level)
logging.captureWarnings(True)
if show_message:
print(f"Loompy v{__version__} by Linnarsson Lab 🌸 (http://linnarssonlab.org & http://loompy.org)")
print()
@cli.command()
@click.argument('loomfile', required=True)
@click.argument('sampleid', required=True)
@click.argument('indexdir', required=True)
@click.argument('metadatafile', required=True)
@click.argument('fastqs', required=True, nargs=-1)
@click.option('--threads', default=os.cpu_count(), help="Number of threads to use")
def fromfq(loomfile: str, sampleid: str, indexdir: str, metadatafile: str, threads: int, fastqs: List[str]) -> None:
logging.info(f"Using {threads} threads.")
create_from_fastq(loomfile, sampleid, list(fastqs), indexdir, metadatafile, threads)
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