From 45697eccdaef310ca3024fbb58ec18247ce856f4 Mon Sep 17 00:00:00 2001
From: czerno <fotakisg@gmail.com>
Date: Fri, 19 Mar 2021 11:42:12 +0100
Subject: [PATCH] pep seq '?' symbol bug hotfix

---
 Docker/source/cleave_peptides.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/Docker/source/cleave_peptides.py b/Docker/source/cleave_peptides.py
index 5825533..9dddbe6 100644
--- a/Docker/source/cleave_peptides.py
+++ b/Docker/source/cleave_peptides.py
@@ -135,10 +135,11 @@ def window_onslaught(
                     )  # Cut the part of gene 1 that doesn't span the junction
                     seq3 = seq[splitat:].replace("|", "")
                     peps = rolling_window(seq3, winSize)
-                    if "?" in pep:
-                        pass
-                    else:
-                        peptides.append(pep)
+                    for pep in peps:
+                        if "?" in pep:
+                            pass
+                        else:
+                            peptides.append(pep)
                     if not peptides:
                         pass
                     else: