From 6ce5a3fce510cfdbca0d772938c0f91ac1cb8f7d Mon Sep 17 00:00:00 2001
From: BjornFJohansson <bjornjobb@gmail.com>
Date: Sun, 24 Mar 2024 16:32:56 +0000
Subject: [PATCH] user & bugfix amplicon

---
 src/pydna/amplicon.py        |  5 +++--
 src/pydna/user_cloning.py    | 29 +++++++++++++++++++++++++++++
 tests/format_sequences.ipynb | 16 ++++++++--------
 tests/test_USERcloning.py    |  6 ++++++
 tests/test_module_dseq.py    |  3 ++-
 5 files changed, 48 insertions(+), 11 deletions(-)
 create mode 100644 src/pydna/user_cloning.py

diff --git a/src/pydna/amplicon.py b/src/pydna/amplicon.py
index 0e1f1a6c..25e76f53 100755
--- a/src/pydna/amplicon.py
+++ b/src/pydna/amplicon.py
@@ -119,8 +119,9 @@ def figure(self):
         faz = tp[fp.position - fp._fp : fp.position].seq
         raz = tp[rp.position : rp.position + rp._fp].seq
         sp3 = " " * (len(fp.seq) + 3)
-        fzc = tp.seq.rc()[::-1][fp.position - fp._fp : fp.position]
-        rzc = tp.seq.rc()[::-1][rp.position : rp.position + rp._fp]
+        # breakpoint()
+        fzc = tp.seq.crick[::-1][fp.position - fp._fp : fp.position]
+        rzc = tp.seq.crick[::-1][rp.position : rp.position + rp._fp]
         f = f"""
             {" " *ft}5{faz}...{raz}3
              {sp3}{"|" * rp._fp}
diff --git a/src/pydna/user_cloning.py b/src/pydna/user_cloning.py
new file mode 100644
index 00000000..1402c65a
--- /dev/null
+++ b/src/pydna/user_cloning.py
@@ -0,0 +1,29 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+# Copyright 2013-2023 by Björn Johansson.  All rights reserved.
+# This code is part of the Python-dna distribution and governed by its
+# license.  Please see the LICENSE.txt file that should have been included
+# as part of this package.
+
+
+# from abc import ABC, abstractmethod
+# import re
+# from pydna.utils import rc
+
+
+"""
+Nicking & USER cloning
+
+
+CGAuGTCGACTTAGATCTCACAGGCTTTTTTCAAGaCGGCCTTGAATTCAGTCATTTGGATCCGGCCGATC
+GCTACAGCTGAATCTAGAGTGTCCGAAAAAAGTTCTGCCGGAACTTAAGTCAGTAAACCTAGGCCGGCuAG
+
+1. Digest both strands
+2. Collect all linear ssDNA
+3. Anneal all combinations
+4. Keep ones present in original molecule
+5. Rank by stability
+6.
+
+"""
diff --git a/tests/format_sequences.ipynb b/tests/format_sequences.ipynb
index 5915dde1..ebaeb8b4 100755
--- a/tests/format_sequences.ipynb
+++ b/tests/format_sequences.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -14,7 +14,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -31,7 +31,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -41,7 +41,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -50,7 +50,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
@@ -200,9 +200,9 @@
  "metadata": {
   "anaconda-cloud": {},
   "kernelspec": {
-   "display_name": "Python [conda env:bjorn38]",
+   "display_name": "bjorn311",
    "language": "python",
-   "name": "conda-env-bjorn38-py"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -214,7 +214,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.5"
+   "version": "3.11.8"
   }
  },
  "nbformat": 4,
diff --git a/tests/test_USERcloning.py b/tests/test_USERcloning.py
index ad389a92..43e88c79 100644
--- a/tests/test_USERcloning.py
+++ b/tests/test_USERcloning.py
@@ -40,6 +40,12 @@ def test_USER_cloning():
     assert p.seq.crick == "GAUCGGCCGGATCCAAATGACTGAATTCAAGGCCGtCTTGAAAAAAGCCTGTGAGATCTAAGTCGACATCG"
 
 
+
+
+
+
+
+
 # hej = p.seq
 
 # from Bio.SeqFeature import SeqFeature
diff --git a/tests/test_module_dseq.py b/tests/test_module_dseq.py
index 376aa0da..315e4aa8 100644
--- a/tests/test_module_dseq.py
+++ b/tests/test_module_dseq.py
@@ -191,6 +191,7 @@ def cut_and_religate_Dseq(seq_string, enz, top):
     ]
 
     for s in seqs:
+        print(s)
         sek, enz, lin = s
         for i in range(len(sek)):
             zek = sek[i:] + sek[:i]
@@ -591,6 +592,7 @@ def test_Dseq_slicing2():
 
 
 def test_Dseq___getitem__():
+    # test the slicing
     from pydna.dseq import Dseq
 
     s = Dseq("GGATCC", circular=False)
@@ -603,7 +605,6 @@ def test_Dseq___getitem__():
     assert s[5:1:-1] == Dseq("CCTA")
 
     assert t[5:1] == Dseq("CG")
-
     assert s[9:1] == Dseq("")
     assert t[9:1] == Dseq("")