fix some lint

Author: Yenaled

kb_python/config.py

@@ -37,10 +37,10 @@ def get_provided_kallisto_path() -> Optional[str]:
     bin_name = 'kallisto'
     if '_KALLISTO_OPTOFF' in globals():
         if _KALLISTO_OPTOFF:
-            bin_name=f'{bin_name}_optoff'
+            bin_name = f'{bin_name}_optoff'
     if '_KALLISTO_KMER_64' in globals():
         if _KALLISTO_KMER_64:
-            bin_name=f'{bin_name}_k64'
+            bin_name = f'{bin_name}_k64'
     bin_filename = f'{bin_name}.exe' if PLATFORM == 'windows' else bin_name
     path = os.path.join(BINS_DIR, PLATFORM, CPU, 'kallisto', bin_filename)
     if not os.path.isfile(path):
@@ -60,12 +60,14 @@ def get_provided_bustools_path() -> Optional[str]:
         return None
     return path
 
+
 def set_special_kallisto_binary(k64: bool, optoff: bool):
     global _KALLISTO_KMER_64
     global _KALLISTO_OPTOFF
     _KALLISTO_KMER_64 = k64
     _KALLISTO_OPTOFF = optoff
 
+
 def get_compiled_kallisto_path(alias: str = COMPILED_DIR) -> Optional[str]:
     """Finds platform-dependent kallisto binary compiled with `compile`.
 

kb_python/extract.py

@@ -82,13 +82,15 @@ def bustools_extract(
     run_executable(command)
     return {"bus": out_path}
 
+
 def is_gzipped(file_path):
     """
     Checks if a file is gzipped by reading its magic number.
     """
     with open(file_path, 'rb') as file:
         return file.read(2) == b'\x1f\x8b'
 
+
 def read_headers_from_fastq(fastq_file):
     """
     Reads headers from a FASTQ file and returns a set of headers.
@@ -188,22 +190,22 @@ def remove_mm_from_bus(t2g_path, txnames, temp_dir, bus_in):
     ecs_mm, _ = get_mm_ecs(t2g_path, txnames, temp_dir)
 
     if len(ecs_mm) > 0:
-        ## Remove mm ecs from bus file
+        # Remove mm ecs from bus file
         bus_txt = os.path.join(temp_dir, "output.bus.txt")
         bus_txt_no_mm = os.path.join(temp_dir, "output_no_mm.bus.txt")
         bus_no_mm = os.path.join(temp_dir, "output_no_mm.bus")
-    
+
         # Convert bus to txt file
         bustools_text(bus_path=bus_in, out_path=bus_txt, flags=True)
-    
+
         # Remove mm ecs
         bus_df = pd.read_csv(bus_txt, sep="\t", header=None)
         new_bus_df = bus_df[~bus_df[2].isin(ecs_mm)]
         new_bus_df.to_csv(bus_txt_no_mm, sep="\t", index=False, header=None)
-    
+
         # Convert back to bus format
         bustools_fromtext(txt_path=bus_txt_no_mm, out_path=bus_no_mm)
-    
+
         logger.debug(
             f"BUS file without equivalence classes that map to multiple genes saved at {bus_no_mm}"
         )
@@ -223,7 +225,8 @@ def remove_mm_from_mc(t2g_path, txnames, temp_dir):
     ecmap_no_mm = os.path.join(temp_dir, "matrix_no_mm.ec")
 
     logger.debug(
-        f"Replacing transcript entries with -1 for equivalence classes that map to multiple genes from {os.path.join(temp_dir, 'matrix.ec')}"
+        f"Replacing transcript entries with -1 for equivalence classes "
+        "that map to multiple genes from {os.path.join(temp_dir, 'matrix.ec')}"
     )
 
     # Get multimapped equivalence classes
@@ -233,9 +236,10 @@ def remove_mm_from_mc(t2g_path, txnames, temp_dir):
         # Replace transcript entries for multimapped equivalence classes with -1
         ec_df.loc[ec_df[0].isin(ecs_mm), 1] = -1
         ec_df.to_csv(ecmap_no_mm, sep="\t", index=False, header=None)
-    
+
         logger.debug(
-            f"matrix.ec file where transcript entries were replaced with -1 for equivalence classes that map to multiple genes saved at {ecmap_no_mm}"
+            f"matrix.ec file where transcript entries were replaced with -1 for "
+            "equivalence classes that map to multiple genes saved at {ecmap_no_mm}"
         )
 
         return ecmap_no_mm
@@ -271,11 +275,19 @@ def extract(
     targets: Gene or transcript names for which to extract the raw reads that align to the index
     out_dir: Path to output directory
     target_type: 'gene' (default) or 'transcript' -> Defines whether targets are gene or transcript names
-    extract_all: Extracts reads for all genes or transcripts (as defined in target_type), defaults to `False`. Might take a long time to run when the reference index contains a large number of genes. Set targets = None when using extract_all
-    extract_all_fast: Extracts all pseudo-aligned reads, defaults to `False`. Does not break down output by gene/transcript. Set targets = None when using extract_all_fast
-    extract_all_unmapped: Extracts all unmapped reads, defaults to `False`. Set targets = None when using extract_all_unmapped
+    extract_all: Extracts reads for all genes or transcripts (as defined in target_type), defaults to `False`.
+        Might take a long time to run when the reference index contains a large number of genes.
+        Set targets = None when using extract_all
+    extract_all_fast: Extracts all pseudo-aligned reads, defaults to `False`.
+        Does not break down output by gene/transcript.
+        Set targets = None when using extract_all_fast
+    extract_all_unmapped: Extracts all unmapped reads, defaults to `False`.
+        Set targets = None when using extract_all_unmapped
     mm: Also extract reads that multi-mapped to several genes, defaults to `False`
-    t2g_path: Path to transcript-to-gene mapping file (required when mm = False, target_type = 'gene' (and extract_all_fast and extract_all_unmapped = False), OR extract_all = True)
+    t2g_path: Path to transcript-to-gene mapping file
+        (required when mm = False, target_type = 'gene'
+        (and extract_all_fast and extract_all_unmapped = False),
+        OR extract_all = True)
     temp_dir: Path to temporary directory, defaults to `tmp`
     threads: Number of threads to use, defaults to `8`
     aa: Align to index generated from a FASTA-file containing amino acid sequences, defaults to `False`
@@ -287,19 +299,21 @@ def extract(
     """
     if sum([extract_all, extract_all_fast, extract_all_unmapped]) > 1:
         raise ValueError(
-            f"extract_all, extract_all_fast, and/or extract_all_unmapped cannot be used simultaneously"
+            "extract_all, extract_all_fast, and/or extract_all_unmapped cannot be used simultaneously"
         )
 
     if targets is None and not (
         extract_all or extract_all_fast or extract_all_unmapped
     ):
         raise ValueError(
-            f"targets must be provided (unless extract_all, extract_all_fast, or extract_all_unmapped are used to extract all reads)"
+            "targets must be provided "
+            "(unless extract_all, extract_all_fast, or extract_all_unmapped are used to extract all reads)"
         )
 
     if targets and (extract_all or extract_all_fast or extract_all_unmapped):
         logger.warning(
-            f"targets will be ignored since extract_all, extract_all_fast, or extract_all_unmapped is activated which will extract all reads"
+            "targets will be ignored since extract_all, extract_all_fast, or extract_all_unmapped "
+            "is activated which will extract all reads"
         )
 
     if target_type not in ["gene", "transcript"]:
@@ -313,14 +327,16 @@ def extract(
         or extract_all
     ) and (t2g_path is None):
         raise ValueError(
-            "t2g_path must be provided if mm flag is not provided, target_type is 'gene' (and extract_all_fast and extract_all_unmapped are False), OR extract_all is True"
+            "t2g_path must be provided if mm flag is not provided, target_type is 'gene' "
+            "(and extract_all_fast and extract_all_unmapped are False), OR extract_all is True"
         )
 
     # extract_all_unmapped requires bustools version > 0.43.2 since previous versions have a bug in the output fastq format that changes the sequence headers
     bustools_version_tuple = get_bustools_version()
     if extract_all_unmapped and not (0, 43, 2) < bustools_version_tuple:
         raise ValueError(
-            f"extract_all_unmapped requires bustools version > 0.43.2. You are currently using bustools version {'.'.join(str(i) for i in bustools_version_tuple)}."
+            f"extract_all_unmapped requires bustools version > 0.43.2. "
+            "You are currently using bustools version {'.'.join(str(i) for i in bustools_version_tuple)}."
         )
 
     make_directory(out_dir)
@@ -379,7 +395,11 @@ def extract(
             # Save unmapped reads in a separate fastq file
             unmapped_fastq = os.path.join(out_dir, "all_unmapped/1.fastq.gz")
             mapped_fastq = os.path.join(extract_out_folder, "1.fastq.gz")
-            extract_matching_reads_by_header(mapped_fastq, fastq[0] if isinstance(fastq, list) else fastq, unmapped_fastq)
+            extract_matching_reads_by_header(
+                mapped_fastq,
+                fastq[0] if isinstance(fastq, list) else fastq,
+                unmapped_fastq
+            )
 
     else:
         if not mm:

kb_python/main.py

@@ -1597,8 +1597,14 @@ def setup_extract_args(
 
     parser_extract = parser.add_parser(
         'extract',
-        description='Extract sequencing reads that were pseudoaligned to specific genes/transcripts (or extract all reads that were / were not pseudoaligned).',
-        help='Extract sequencing reads that were pseudoaligned to specific genes/transcripts (or extract all reads that were / were not pseudoaligned)',
+        description=(
+            'Extract sequencing reads that were pseudoaligned to specific genes/transcripts '
+            '(or extract all reads that were / were not pseudoaligned).'
+        ),
+        help=(
+            'Extract sequencing reads that were pseudoaligned to specific genes/transcripts '
+            '(or extract all reads that were / were not pseudoaligned)'
+        ),
         parents=[parent]
     )
     parser_extract._actions[0].help = parser_extract._actions[
@@ -1611,7 +1617,8 @@ def setup_extract_args(
         type=str,
         help=(
             'Single fastq file containing the sequencing reads (e.g. in case of 10x data, provide the R2 file).'
-            ' Sequencing technology will be treated as bulk here since barcode and UMI tracking is not necessary to extract reads.'
+            ' Sequencing technology will be treated as bulk here since barcode and UMI tracking '
+            'is not necessary to extract reads.'
         )
     )
     required_extract.add_argument(
@@ -1643,16 +1650,19 @@ def setup_extract_args(
     parser_extract.add_argument(
         '--extract_all',
         help=(
-            'Extracts all reads that pseudo-aligned to any gene or transcript (as defined by target_type) (breaks down output by gene/transcript). '
-            'Using extract_all might take a long time to run when there are a large number of genes/transcripts in the index.'
+            'Extracts all reads that pseudo-aligned to any gene or transcript (as defined by target_type) '
+            '(breaks down output by gene/transcript). '
+            'Using extract_all might take a long time to run when there are a large number of '
+            'genes/transcripts in the index.'
         ),
         action='store_true',
         default=False
     )
     parser_extract.add_argument(
         '--extract_all_fast',
         help=(
-            'Extracts all reads that pseudo-aligned (does not break down output by gene/transcript; output saved in the "all" folder).'
+            'Extracts all reads that pseudo-aligned (does not break down output by gene/transcript; '
+            'output saved in the "all" folder).'
         ),
         action='store_true',
         default=False
@@ -1677,7 +1687,9 @@ def setup_extract_args(
         '-g',
         metavar='T2G',
         help=(
-            'Path to transcript-to-gene mapping file (required when mm = False, target_type = "gene" (and extract_all_fast and extract_all_unmapped = False), OR extract_all = True).'
+            'Path to transcript-to-gene mapping file '
+            '(required when mm = False, target_type = "gene" '
+            '(and extract_all_fast and extract_all_unmapped = False), OR extract_all = True).'
         ),
         type=str,
     )
@@ -1837,7 +1849,7 @@ def main():
     # Set binary paths
     if args.command in ('ref', 'count', 'extract') and ('dry_run' not in args
                                                         or not args.dry_run):
-                                                          
+
         use_kmer64 = False
         opt_off = False
         if args.k and args.k > 32:

kb_python/utils.py

@@ -721,7 +721,7 @@ def overlay_anndatas(
         ambiguous_intersection = adata_ambiguous[obs_idx][:, var_idx]
         a_layers.update({'ambiguous': ambiguous_intersection.X})
         sum_X = sum_X + ambiguous_intersection.X
-    
+
     df_obs = unspliced_intersection.obs
     df_var = unspliced_intersection.var
     return anndata.AnnData(