Fix stripping of _R_ pattern

Using lstrip() led to unwanted behavior
edgardomortiz · Feb 14, 2024 · 176c617 · 176c617
1 parent 2f83164
commit 176c617
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Showing 2 changed files with 8 additions and 2 deletions.
diff --git a/captus/bioformats.py b/captus/bioformats.py
@@ -3488,7 +3488,10 @@ def rehead_root_msa(fasta_in: Path, fasta_out: Path, outgroup: list, remove_R_=F
         aligned = {}
         aligned_w_R_ = fasta_to_dict(fasta_out)
         for seq_name in aligned_w_R_:
-            aligned[seq_name.lstrip("_R_")] = aligned_w_R_[seq_name]
+            if seq_name.startswith("_R_"):
+                aligned[seq_name[3:]] = aligned_w_R_[seq_name]
+            else:
+                aligned[seq_name] = aligned_w_R_[seq_name]
     else:
         aligned = fasta_to_dict(fasta_out)
 

diff --git a/captus/cluster.py b/captus/cluster.py
@@ -970,7 +970,10 @@ def cleanup_fastas(all_fastas: list):
         intermediate_fasta = fasta_to_dict(intermediate_fasta_path)
         output_fasta = {}
         for seq_name in intermediate_fasta:
-            new_seq_name = seq_name.lstrip("_R_")
+            if seq_name.startswith("_R_"):
+                new_seq_name = seq_name[3:]
+            else:
+                new_seq_name = seq_name
             output_fasta[new_seq_name] = {
                 "sequence": intermediate_fasta[seq_name]["sequence"],
                 "description": input_fasta[new_seq_name]["description"],