fix linting

deeptools · Apr 22, 2024 · 799ca0d · 799ca0d
1 parent 1b33c58
commit 799ca0d
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Showing 3 changed files with 5 additions and 6 deletions.
diff --git a/hicexplorer/chicAggregateStatistic.py b/hicexplorer/chicAggregateStatistic.py
@@ -68,7 +68,7 @@ def filter_scores_target_list(pScoresDictionary, pTargetFType, pTargetPosDict, p
     accepted_scores = {}
     same_target_dict = {}
     target_regions_intervaltree = None
-    #newly added
+    # newly added
     if pTargetFType == 'hdf5':
         # read hdf content for this specific combination
         targetFileHDF5Object = h5py.File(pTargetFile, 'r')
@@ -82,7 +82,7 @@ def filter_scores_target_list(pScoresDictionary, pTargetFType, pTargetPosDict, p
         start_list = pTargetPosDict[pTargetList[-1]]['start_list']
         end_list = pTargetPosDict[pTargetList[-1]]['end_list']
     elif pTargetFType == 'bed3':
-         target_regions_intervaltree = pTargetIntervalTree
+        target_regions_intervaltree = pTargetIntervalTree
     else:
         log.error('No target list given.')
         raise Exception('No target list given.')
@@ -349,7 +349,7 @@ def main(args=None):
             targetList = [args.targetFile]
             target_ftype = 'bed3'
         else:
-            log.error('BED of targets list must have 3 or 4 columns')    
+            log.error('BED of targets list must have 3 or 4 columns')
 
     if len(keys_interactionFile) > 1:
 

diff --git a/hicexplorer/hicCorrectMatrix.py b/hicexplorer/hicCorrectMatrix.py
@@ -677,8 +677,7 @@ def main(args=None):
         ma.maskBins(outlier_regions)
         total_filtered_out = set(outlier_regions)
         print(outlier_regions, "Bins that are MAD outliers ({:.2f}%) "
-                            "out of {}".format(pct_outlier, ma.matrix.shape[0]))
-
+              "out of {}".format(pct_outlier, ma.matrix.shape[0]))
 
         if args.sequencedCountCutoff and 0 < args.sequencedCountCutoff < 1:
             chrom, _, _, coverage = zip(*ma.cut_intervals)

diff --git a/hicexplorer/test/general/test_chicAggregateStatistic.py b/hicexplorer/test/general/test_chicAggregateStatistic.py
@@ -190,4 +190,4 @@ def test_target_list_bed4():
             for data in aggregateFileH5Object['c_adj_norm_t_adj_norm']['t_adj_norm'][chromosome][gene]:
                 assert data in ['chromosome', 'end_list', 'gene_name', 'raw_target_list', 'relative_distance_list', 'start_list', 'sum_of_interactions']
 
-    aggregateFileH5Object.close()
+    aggregateFileH5Object.close()