diff --git a/bedboss/bbuploader/cli.py b/bedboss/bbuploader/cli.py index 04fd90e..fb79413 100644 --- a/bedboss/bbuploader/cli.py +++ b/bedboss/bbuploader/cli.py @@ -1,11 +1,11 @@ import typer +from bedboss._version import __version__ app_bbuploader = typer.Typer( pretty_exceptions_short=False, pretty_exceptions_show_locals=False, help="Automatic BEDbase uploader for GEO data", ) -from bedboss._version import __version__ @app_bbuploader.command( diff --git a/bedboss/bbuploader/main.py b/bedboss/bbuploader/main.py index 8eb173c..24ab171 100644 --- a/bedboss/bbuploader/main.py +++ b/bedboss/bbuploader/main.py @@ -96,7 +96,7 @@ def upload_all( gse_status.status == STATUS.FAIL or gse_status.status == STATUS.PROCESSING ) and not run_failed: - _LOGGER.info(f"Reprocessing of failed set to false, exiting.") + _LOGGER.info("Reprocessing of failed set to false, exiting.") continue elif ( @@ -278,7 +278,7 @@ def upload_gse( gse_status.status == STATUS.FAIL or gse_status.status == STATUS.PROCESSING ) and not run_failed: - _LOGGER.info(f"Reprocessing of failed set to false, exiting.") + _LOGGER.info("Reprocessing of failed set to false, exiting.") exit() elif ( diff --git a/bedboss/bedclassifier/bedclassifier.py b/bedboss/bedclassifier/bedclassifier.py index cb58842..68eb0ed 100644 --- a/bedboss/bedclassifier/bedclassifier.py +++ b/bedboss/bedclassifier/bedclassifier.py @@ -45,7 +45,7 @@ def get_bed_type(bed: str, no_fail: Optional[bool] = True) -> Tuple[str, str]: if row_count > 0: _LOGGER.info(f"Skipped {row_count} rows to parse bed file {bed}") break - except UnicodeDecodeError as e: + except UnicodeDecodeError: try: df = pd.read_csv( bed, diff --git a/bedboss/bedmaker/bedmaker.py b/bedboss/bedmaker/bedmaker.py index 944956a..b0db50a 100755 --- a/bedboss/bedmaker/bedmaker.py +++ b/bedboss/bedmaker/bedmaker.py @@ -78,7 +78,7 @@ def make_bigbed( try: chrom_sizes = get_chrom_sizes(genome=genome, rfg_config=rfg_config) except MissingGenomeError: - _LOGGER.error(f"Could not find Genome in refgenie. Skipping...") + _LOGGER.error("Could not find Genome in refgenie. Skipping...") chrom_sizes = "" temp = os.path.join(output_path, next(tempfile._get_candidate_names())) @@ -391,7 +391,7 @@ def make_all( chrom_sizes=chrom_sizes, pm=pm, ) - except BedBossException as e: + except BedBossException: output_bigbed = None if pm_clean: pm.stop_pipeline() diff --git a/bedboss/bedmaker/const.py b/bedboss/bedmaker/const.py index cf8dae7..78a934e 100644 --- a/bedboss/bedmaker/const.py +++ b/bedboss/bedmaker/const.py @@ -1,5 +1,3 @@ -from enum import Enum - BED_TO_BIGBED_PROGRAM = "bedToBigBed" # BED_TO_BIGBED_PROGRAM = "/home/bnt4me/virginia/repos/bedbase_all/bedboss/bedToBigBed" BIGBED_TO_BED_PROGRAM = "bigBedToBed" diff --git a/bedboss/cli.py b/bedboss/cli.py index e73dddf..95d1b77 100644 --- a/bedboss/cli.py +++ b/bedboss/cli.py @@ -244,7 +244,7 @@ def make_bed( ) -@app.command(help=f"Create a bigbed files form a bed file") +@app.command(help="Create a bigbed files form a bed file") def make_bigbed( bed_file: str = typer.Option( ..., diff --git a/bedboss/models.py b/bedboss/models.py index b0f98ac..ddbae26 100644 --- a/bedboss/models.py +++ b/bedboss/models.py @@ -1,6 +1,6 @@ import pathlib from enum import Enum -from typing import Dict, Union +from typing import Union import pypiper from bbconf.models.bed_models import (