fixed linting issues

biocore · Jun 30, 2024 · 2f12569 · 2f12569
1 parent aa75810
commit 2f12569
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Showing 2 changed files with 18 additions and 12 deletions.
diff --git a/micov/_io.py b/micov/_io.py
@@ -10,9 +10,9 @@
 import gzip
 
 from ._cov import compress, coverage_percent
-from ._constants import (BED_COV_SCHEMA, GENOME_COVERAGE_SCHEMA, 
-                         COLUMN_GENOME_ID, COLUMN_LENGTH, COLUMN_TAXONOMY, 
-                         SAM_SUBSET_SCHEMA, COLUMN_CIGAR, COLUMN_STOP, 
+from ._constants import (BED_COV_SCHEMA, GENOME_COVERAGE_SCHEMA,
+                         COLUMN_GENOME_ID, COLUMN_LENGTH, COLUMN_TAXONOMY,
+                         SAM_SUBSET_SCHEMA, COLUMN_CIGAR, COLUMN_STOP,
                          COLUMN_START, COLUMN_SAMPLE_ID)
 from ._convert import cigar_to_lens
 
@@ -177,7 +177,8 @@ def _test_has_header_taxonomy(line):
 
     if line.startswith('#'):
         has_header = True
-    elif line.split('\t')[0] in genome_id_columns and line.split('\t')[1] in taxonomy_columns:
+    elif line.split('\t')[0] in genome_id_columns and \
+        line.split('\t')[1] in taxonomy_columns:
         has_header = True
     else:
         has_header = False
@@ -221,10 +222,10 @@ def parse_taxonomy(taxonomy):
     genome_ids = df[genome_id_col]
     if len(genome_ids) != len(set(genome_ids)):
         raise ValueError(f"'{genome_id_col}' is not unique")
-    
+
     rename = {genome_id_col: COLUMN_GENOME_ID,
               taxonomy_col: COLUMN_TAXONOMY}
-    
+
     return df[[genome_id_col, taxonomy_col]].rename(rename)
 
 

diff --git a/micov/cli.py b/micov/cli.py
@@ -7,8 +7,8 @@
 import sys
 import tqdm
 from ._io import (parse_genome_lengths, parse_taxonomy, set_taxonomy_as_id,
-                  parse_qiita_coverages, parse_sam_to_df, write_qiita_cov, 
-                  parse_sample_metadata, compress_from_stream, 
+                  parse_qiita_coverages, parse_sam_to_df, write_qiita_cov,
+                  parse_sample_metadata, compress_from_stream,
                   parse_bed_cov_to_df)
 from ._cov import coverage_percent
 from ._convert import cigar_to_lens
@@ -83,7 +83,8 @@ def qiita_coverage(qiita_coverages, samples_to_keep, samples_to_ignore,
 @click.option('--lengths', type=click.Path(exists=True), required=False,
               help='Genome lengths, if provided compute coverage')
 @click.option('--taxonomy', type=click.Path(exists=True), required=False,
-              help='Genome taxonomy, if provided show species in coverage percentage. Only works when --length is provided')
+              help=('Genome taxonomy, if provided show species in coverage '
+                    'percentage. Only works when --length is provided'))
 def compress(data, output, disable_compression, lengths, taxonomy):
     """Compress BAM/SAM/BED mapping data.
 
@@ -97,7 +98,7 @@ def compress(data, output, disable_compression, lengths, taxonomy):
     if lengths is not None:
         lengths = parse_genome_lengths(lengths)
 
-        if taxonomy is not None: 
+        if taxonomy is not None:
             taxonomy = parse_taxonomy(taxonomy)
 
     # compress data in blocks to avoid loading full mapping data into memory
@@ -115,8 +116,12 @@ def compress(data, output, disable_compression, lengths, taxonomy):
         if taxonomy is None:
             genome_coverage.write_csv(output, separator='\t', include_header=True)
         else:
-            genome_coverage_with_taxonomy = set_taxonomy_as_id(genome_coverage, taxonomy)
-            genome_coverage_with_taxonomy.write_csv(output, separator='\t', include_header=True)
+            genome_coverage_with_taxonomy = set_taxonomy_as_id(
+                genome_coverage, taxonomy
+                )
+            genome_coverage_with_taxonomy.write_csv(
+                output, separator='\t', include_header=True
+                )
 
 
 @cli.command()