cna - fix pandas dtype warning

sigven · Dec 15, 2023 · 361276b · 361276b
1 parent c809907
commit 361276b
Showing 1 changed file with 3 additions and 1 deletion.
diff --git a/pcgr/cna.py b/pcgr/cna.py
@@ -142,13 +142,15 @@ def annotate_cna_segments(output_fname: str,
 
     ## Mark copy number amplifications (threshold defined by user) in input
     cna_query_segment_df['aberration_key'] = 'nan'
+    cna_query_segment_df['loss_cond'] = True
     cna_query_segment_df.loc[cna_query_segment_df['n_major'] + cna_query_segment_df['n_minor'] < n_copy_amplifications,"amp_cond"] = False
     cna_query_segment_df.loc[cna_query_segment_df['n_major'] + cna_query_segment_df['n_minor'] >= n_copy_amplifications,"amp_cond"] = True
 
     cna_query_segment_df.loc[cna_query_segment_df.amp_cond, 'aberration_key'] =  \
         cna_query_segment_df.loc[cna_query_segment_df.amp_cond, 'entrezgene'].astype(str) + '_amplification'
 
     ## Mark homozygous deletions in input
+    cna_query_segment_df['amp_cond'] = True
     cna_query_segment_df.loc[cna_query_segment_df['n_major'] + cna_query_segment_df['n_minor'] > 0,"loss_cond"] = False
     cna_query_segment_df.loc[cna_query_segment_df['n_major'] + cna_query_segment_df['n_minor'] == 0,"loss_cond"] = True
 
@@ -181,7 +183,7 @@ def annotate_cna_segments(output_fname: str,
             cna_query_segment_df['N_MAJOR'].astype(str), sep=":").str.cat(
                 cna_query_segment_df['N_MINOR'].astype(str), sep=":")
 
-    cna_query_segment_bed['SAMPLE_ID'] = sample_id
+    cna_query_segment_df['SAMPLE_ID'] = sample_id
     cna_query_segment_df.to_csv(output_fname, sep="\t", header=True, index=False)
 
     return 0