more work in shard

YeoLab · Jul 24, 2024 · a7565e9 · a7565e9
1 parent 63c2ce4
commit a7565e9
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Showing 2 changed files with 18 additions and 24 deletions.
diff --git a/marine.py b/marine.py
@@ -385,6 +385,7 @@ def run(bam_filepath, annotation_bedfile_path, output_folder, contigs=[], num_in
     # Filtering steps
     if not final_path_already_exists:
         print("Filtering..")
+
         all_edit_info_unique_position_with_coverage_df = pd.read_csv('{}/final_edit_info.tsv'.format(output_folder), sep='\t',
                                                                      index_col=0,
                                                                      names=[
@@ -393,32 +394,9 @@ def run(bam_filepath, annotation_bedfile_path, output_folder, contigs=[], num_in
                                                                          'coverage'],
                                                                      dtype={'base_quality': int, 'dist_from_end': int, 'contig': str})
 
-        print("Deduplicating....")
-        distinguishing_columns = [
-            "barcode",
-            "contig",
-            "position",
-            "ref",
-            "alt",
-            "read_id",
-            "strand",
-            "mapping_quality",
-        ]
-        if not skip_coverage:
-            distinguishing_columns.append("coverage")
-
-        all_edit_info_filtered_deduped = all_edit_info_unique_position_with_coverage_df.drop_duplicates(
-            distinguishing_columns)[distinguishing_columns]
-
         pretty_print("\tNumber of edits after filtering:\n\t{}".format(len(all_edit_info_unique_position_with_coverage_df)))
-        pretty_print("\tNumber of edits after deduplicating:\n\t{}".format(len(all_edit_info_filtered_deduped)))    
-        all_edit_info_filtered_deduped.to_csv('{}/final_filtered_edit_info.tsv'.format(output_folder), 
-                                         sep='\t', index=False)
-
-        all_edit_info_unique_position_with_coverage_deduped_df = pd.read_csv('{}/final_filtered_edit_info.tsv'.format(output_folder), sep='\t', dtype={"contig": str})
-
 
-        all_edit_info_filtered_pl = pl.from_pandas(all_edit_info_unique_position_with_coverage_deduped_df)
+        all_edit_info_filtered_pl = pl.from_pandas(all_edit_info_unique_position_with_coverage_df)
 
         final_site_level_information_df = generate_site_level_information(all_edit_info_filtered_pl, skip_coverage=skip_coverage)
         pretty_print("\tNumber of unique edit sites:\n\t{}".format(len(final_site_level_information_df)))

diff --git a/src/utils.py b/src/utils.py
@@ -417,6 +417,7 @@ def filter_output_df(output_df, filters, output_filename):
         "base_quality",
         "mapping_quality"
     ]
+
 
     all_edit_info_unique_position_df = filtered_output_df.drop_duplicates(distinguishing_columns)[distinguishing_columns]
 
@@ -430,8 +431,23 @@ def filter_output_df(output_df, filters, output_filename):
         read_edits = all_edit_info_unique_position_with_coverage_df.groupby('read_id').count().sort_values('barcode')
         all_edit_info_unique_position_with_coverage_df = all_edit_info_unique_position_with_coverage_df[all_edit_info_unique_position_with_coverage_df.read_id.isin(read_edits[read_edits['barcode'] <= max_edits_per_read].index)]
 
+    distinguishing_columns = [
+            "barcode",
+            "contig",
+            "position",
+            "ref",
+            "alt",
+            "read_id",
+            "strand",
+            "mapping_quality",
+    ]
+
+    all_edit_info_unique_position_with_coverage_df = all_edit_info_unique_position_with_coverage_df.drop_duplicates(
+            distinguishing_columns)[distinguishing_columns]
+
     filter_stats['filtered'] = len(all_edit_info_unique_position_with_coverage_df)
 
+
     all_edit_info_unique_position_with_coverage_df.to_csv(output_filename, sep='\t', header=False)
 
     return filter_stats