From becec350a416bf9425d2b6e07e89fe4a11b7c118 Mon Sep 17 00:00:00 2001 From: Manuel Lera Ramirez Date: Mon, 5 Feb 2024 13:00:07 +0100 Subject: [PATCH] closes #197, but two tests still fail --- poetry.lock | 4156 ++++++++++++------------------- pyproject.toml | 4 +- src/pydna/amplify.py | 5 +- tests/test_module_dseqrecord.py | 2 + 4 files changed, 1561 insertions(+), 2606 deletions(-) diff --git a/poetry.lock b/poetry.lock index b0033792..0b169412 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,48 +1,48 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. 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[tool.poetry.extras] clipboard = ["pyperclip"] download = ["pyparsing", "requests"] diff --git a/src/pydna/amplify.py b/src/pydna/amplify.py index 200cfb7b..042a50a6 100644 --- a/src/pydna/amplify.py +++ b/src/pydna/amplify.py @@ -354,7 +354,10 @@ def products(self): tpl = self.template else: continue - prd = _Dseqrecord(fp) + tpl[fp.position : rp.position] + _Dseqrecord(rp).reverse_complement() + if tpl.circular and fp.position == rp.position: + prd = _Dseqrecord(fp) + _Dseqrecord(rp).reverse_complement() + else: + prd = _Dseqrecord(fp) + tpl[fp.position : rp.position] + _Dseqrecord(rp).reverse_complement() prd.features = feats full_tmpl_features = [ f for f in self.template.features if f.location.start == 0 and f.location.end == len(self.template) diff --git a/tests/test_module_dseqrecord.py b/tests/test_module_dseqrecord.py index 16e8f6b5..73213ff3 100644 --- a/tests/test_module_dseqrecord.py +++ b/tests/test_module_dseqrecord.py @@ -1605,6 +1605,8 @@ def test_figure(): assert circularDseqrecord.extract_feature(0).seq == feat a22, b22 = circularDseqrecord.cut(KpnI, Bsp120I) + + # Passes the tests if changed to "Dseqrecord(-18)\n cgatcgatcG \ncatg\x1b[48;5;11mgctagctagC\x1b[0mCCGG" assert ( b22.figure() == "Dseqrecord(-18)\n cgatcgatcG \ncatg\x1b[48;5;11mgctag\x1b[0m\x1b[48;5;11mctagC\x1b[0mCCGG"