added default length settings as per code review

bokulich-lab · Nov 19, 2024 · 4a4030a · 4a4030a
1 parent dac2412
commit 4a4030a
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Showing 2 changed files with 10 additions and 10 deletions.
diff --git a/rescript/extract_seq_segments.py b/rescript/extract_seq_segments.py
@@ -15,8 +15,8 @@ def extract_seq_segments(input_sequences: DNAFASTAFormat,
                          reference_segment_sequences: DNAFASTAFormat,
                          perc_identity: float = 0.7,
                          target_coverage: float = 0.9,
-                         min_seq_len: int = None,
-                         max_seq_len: int = None,
+                         min_seq_len: int = 32,
+                         max_seq_len: int = 50000,
                          threads: int = 1
                          ) -> (DNAFASTAFormat, DNAFASTAFormat):
     # Note: the `--db` is actually comprised of the short amplicon
@@ -44,13 +44,15 @@ def extract_seq_segments(input_sequences: DNAFASTAFormat,
                '--id', str(perc_identity),
                '--target_cov', str(target_coverage),
                '--strand', 'plus',
+               '--minseqlength', str(min_seq_len),
+               '--maxseqlength', str(max_seq_len),
                '--threads', str(threads),
                '--qmask', 'none',
                '--qsegout', extr_f.name,
                '--notmatched', no_match_f.name]
-        if min_seq_len:
-            cmd += ['--minseqlength', '%i' % min_seq_len]
-        if max_seq_len:
-            cmd += ['--maxseqlength', '%i' % max_seq_len]
+        # if min_seq_len:
+        #     cmd += ['--minseqlength', '%i' % min_seq_len]
+        # if max_seq_len:
+        #     cmd += ['--maxseqlength', '%i' % max_seq_len]
         run_command(cmd)
     return (extr_seq_segs, no_matches)
diff --git a/rescript/plugin_setup.py b/rescript/plugin_setup.py
@@ -1154,12 +1154,10 @@
                                    'from \'input-sequences\'.',
                 'min_seq_len': 'Minimum length of reference sequence segment '
                                'allowed for searching. Any sequence less than '
-                               'this will be discarded. If not set, default '
-                               'program settings will be used.',
+                               'this will be discarded.',
                 'max_seq_len': 'Maximum length of reference sequence segment '
                                'allowed for searching. Any sequence greater '
-                               'than this will be discarded. If not set, '
-                               'default program settings will be used.'},
+                               'than this will be discarded.'},
     output_descriptions={
         'extracted_sequence_segments': 'Extracted sequence segments '
                                        'from \'input-sequences\' '