diff --git a/tests/test_module_dseq.py b/tests/test_module_dseq.py index aaf8e2a2..50c36818 100644 --- a/tests/test_module_dseq.py +++ b/tests/test_module_dseq.py @@ -116,15 +116,15 @@ def test_initialization(): obj2 = Dseq("gata") - assert obj2.circular == False + assert obj2.circular is False - l = Dseq("gt") - c = l.looped() + ln = Dseq("gt") + c = ln.looped() - assert not l.circular + assert not ln.circular assert c.circular - assert Dseq("gt", circular=False) == l + assert Dseq("gt", circular=False) == ln assert Dseq("gt", circular=True) == c assert Dseq.from_string("A") == Dseq("A") @@ -154,6 +154,9 @@ def test_initialization(): ) assert obj3.ovhg == 1 + assert Dseq.from_dsiupac("PEXIaaaQFZJ") == Dseq("GATCaaa", "CTAGttt", -4) + assert Dseq.from_dsiupac("QFZJaaaPEXI") == Dseq("aaaGATC", "tttCTAG", 4) + def test_cut_around_and_religate(): from pydna.dseq import Dseq @@ -218,7 +221,7 @@ def test_Dseq_cutting_adding(): ovhg=0, ) - f, d, l = c.cut((EcoRI, PstI)) + f, d, l_ = c.cut((EcoRI, PstI)) assert d.watson == "GtcatctactatcatcgtagcgtactgatctattctgctgctcatcatcggtactctctataattatatatatatgcgcgtG" assert d.crick == "AATTCacgcgcatatatatataattatagagagtaccgatgatgagcagcagaatagatcagtacgctacgatgatagtagatgaCTGCA" @@ -554,11 +557,12 @@ def test_dseq(): def test_Dseq_slicing(): from pydna.dseq import Dseq - from pydna.readers import read - from pydna.utils import eq - from Bio.Seq import Seq - from Bio.SeqRecord import SeqRecord as Srec + # from pydna.readers import read + # from pydna.utils import eq + + # from Bio.Seq import Seq + # from Bio.SeqRecord import SeqRecord as Srec from Bio.Restriction import BamHI a = Dseq("ggatcc", "ggatcc", 0) @@ -947,7 +951,7 @@ def test_apply_cut(): def test_cutsite_is_valid(): from pydna.dseq import Dseq - from Bio.Restriction import EcoRI, BsaI, PacI, NmeDI, Acc65I, NotI, BamHI, EcoRV + from Bio.Restriction import EcoRI, PacI, NmeDI, EcoRV # Works for circular case seqs = ["GAATTC", "TTAATTAAC", "GATATC"]