From f20d4c91b09c1fc7c461fe869aad3ea0d810110a Mon Sep 17 00:00:00 2001
From: rdenise <remi.denise@gmail.com>
Date: Tue, 30 Jul 2024 11:45:26 +0100
Subject: [PATCH] :bug: Modification to apply the blast command modified to all
 similarity module

---
 taxmyphage/actions.py | 1 +
 taxmyphage/pmv.py     | 6 ++++--
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/taxmyphage/actions.py b/taxmyphage/actions.py
index 367ebb4..2a8dee1 100644
--- a/taxmyphage/actions.py
+++ b/taxmyphage/actions.py
@@ -315,6 +315,7 @@ def clustering_on_genomic_similarity(args: Namespace, threads: int, verbose: boo
         verbose=verbose,
         blastn_exe=args.blastn,
         makeblastdb_exe=args.makeblastdb,
+        similarity_module=True,
     )
 
     dfT, pmv_outfile = pmv.run()
diff --git a/taxmyphage/pmv.py b/taxmyphage/pmv.py
index c8d6db7..cc8435a 100755
--- a/taxmyphage/pmv.py
+++ b/taxmyphage/pmv.py
@@ -40,6 +40,7 @@ def __init__(
         blastn_exe: str = "blastn",
         makeblastdb_exe: str = "makeblastdb",
         output_dir: str = "",
+        similarity_module: bool = False,
     ):
         """
         Args:
@@ -53,6 +54,7 @@ def __init__(
             blastn_exe (str, optional): Path to the blastn executable. Defaults to "blastn".
             makeblastdb_exe (str, optional): Path to the makeblastdb executable. Defaults to "makeblastdb".
             output_dir (str, optional): Path to the output directory. Defaults to "".
+            similarity_module (bool, optional): Whether to use the similarity module. Defaults to False.
             
         Returns:
             None
@@ -72,7 +74,7 @@ def __init__(
         self.dfT = pd.DataFrame()
         self.db_blast = reference
         self.blastn_result_file = ''
-        self.similarity_identical = file == reference
+        self.similarity_module = similarity_module
 
         self.existing_files()
 
@@ -202,7 +204,7 @@ def blastn(self):
             self.result_dir, os.path.basename(self.file) + ".blastn_vs2_self.tab.gz"
         )
         if not os.path.exists(outfile):
-            if self.similarity_identical:
+            if self.similarity_module:
                 cmd = (
                     f'{self.blastn_exe} -evalue 1 -max_target_seqs 10000 -num_threads {self.nthreads} '
                     f'-word_size 7 -reward 2 -penalty -3 -gapopen 5 -gapextend 2 -query {self.file} '