cleaning

Author: khoroshevskyi

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(

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 (

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,

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()

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"

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(
         ...,

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 (