Merge pull request #64 from IBM/rfd-dev

Bug fix: peptides similarity support for None df_target
IBM · Nov 11, 2024 · 1c5d789 · 1c5d789
2 parents 3b81d16 + c12a6c8
commit 1c5d789
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Showing 2 changed files with 8 additions and 4 deletions.
diff --git a/hestia/similarity.py b/hestia/similarity.py
@@ -680,11 +680,12 @@ def _medium_alignment(df_query, df_target, tmp_dir,
                         dbtype, db_target_file, '-v', '1',
                         f'{tmp_dir}/db_target'])
 
-        subprocess.run(['mmseqs', 'search',  f'{tmp_dir}/db_query',
+        subprocess.run(['mmseqs', 'search', f'{tmp_dir}/db_query',
                         f'{tmp_dir}/db_target', f'{tmp_dir}/align_db',
                         f'{tmp_dir}/tmp', '--alignment-mode', '3',
                         '--seq-id-mode', denominator, '--search-type', '1',
-                        '--prefilter-mode', '2', '-s', '2', '-v', mmseqs_v,
+                        '--prefilter-mode', '2', '-s', '2',
+                        '-v', str(mmseqs_v),
                         '--threads', str(threads), '--mask', '0',
                         '--comp-bias-corr', '0',
                         '-e', '1e7'])
@@ -705,6 +706,8 @@ def _medium_alignment(df_query, df_target, tmp_dir,
     os.mkdir(tmp_dir)
 
     df_query['seq_len'] = df_query[field_name].map(len)
+    if df_target is None:
+        df_target = df_query
     normal_df_query = df_query[df_query['seq_len'] > 20]
     medium_df_query = df_query[(df_query['seq_len'] > 8) &
                                (df_query['seq_len'] <= 20)]
@@ -739,7 +742,8 @@ def _medium_alignment(df_query, df_target, tmp_dir,
         medium_simdf = pd.DataFrame()
     if len(small_df_query) > 0:
         small_simdf = _small_alignment(
-            df_query=small_df_query, df_target=df_target, field_name=field_name
+            df_query=small_df_query, df_target=df_target, field_name=field_name,
+            denominator=denominator
         )
     else:
         small_simdf = pd.DataFrame()

diff --git a/setup.py b/setup.py
@@ -48,6 +48,6 @@
     test_suite='tests',
     tests_require=test_requirements,
     url='https://github.com/IBM/Hestia-OOD',
-    version='0.0.32',
+    version='0.0.33',
     zip_safe=False,
 )