def cut_and_religate_Dseq(seq_string, enz, top):
ds = Dseq(seq_string, linear=top)
frags = list(ds.cut(enz))
if not frags:
return
a = frags.pop(0)
for f in frags:
a += f
if not top:
a = a.looped()
assert eq(a, ds)
def test_eq():
from pydna.dseqrecord import Dseqrecord
from pydna.utils import eq
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
assert eq( "AAA" ,"TTT", linear = True )
assert eq( "AAA" ,"TTT", linear = False)
assert eq( "aAA" ,"TtT", linear = True )
assert eq( "AAa" ,"TtT", linear = False)
assert eq( "ATA" ,"AAT", circular = True )
assert not eq( "ATA" ,"AAT", circular = False)
assert eq( "AAA" ,"AAA", linear = True )
assert eq( "AAA" ,"AAA", linear = False)
assert eq( "ATA" ,Seq("AAT"), circular = True )
assert not eq( "ATA" ,Seq("AAT"), circular = False)
assert eq( "AAA" ,Seq("AAA"), linear = True )
assert eq( "AAA" ,Seq("AAA"), linear = False)
assert eq( "ATA" ,SeqRecord("AAT"), circular = True )
assert not eq( "ATA" ,SeqRecord("AAT"), circular = False)
assert eq( "AAA" ,SeqRecord("AAA"), linear = True )
assert eq( "AAA" ,SeqRecord("AAA"), linear = False)
assert eq( "ATA" ,Dseqrecord("AAT"), circular = True )
assert not eq( "ATA" ,Dseqrecord("AAT"), circular = False)
assert eq( "AAA" ,Dseqrecord("AAA"), linear = True )
assert eq( "AAA" ,Dseqrecord("AAA"), linear = False)
assert eq( Seq("ATA") ,SeqRecord("AAT"), circular = True )
assert not eq( Seq("ATA") ,SeqRecord("AAT"), circular = False)
assert eq( Seq("AAA") ,SeqRecord("AAA"), linear = True )
assert eq( Seq("AAA") ,SeqRecord("AAA"), linear = False)
assert eq( Seq("ATA") ,Dseqrecord("AAT"), circular = True )
assert not eq( Seq("ATA") ,Dseqrecord("AAT"), circular = False)
assert eq( Seq("AAA") ,Dseqrecord("AAA"), linear = True )
assert eq( Seq("AAA") ,Dseqrecord("AAA"), linear = False)
assert eq( Dseqrecord("AAA",circular=False) ,Dseqrecord("AAA",circular=False))
assert eq( Dseqrecord("AAA",circular=True) ,Dseqrecord("AAA",circular=True))
assert not eq( Dseqrecord("ATA",circular=False) ,Dseqrecord("AAT",circular=False))
assert eq( Dseqrecord("ATA",circular=True) ,Dseqrecord("AAT",circular=True))
with pytest.raises(ValueError):
eq(Dseqrecord("ATA",circular=True), Dseqrecord("ATA",circular=False))
assert not eq(Dseqrecord("ATA",circular=True), Dseqrecord("ATAA",circular=True))
assert eq(Dseqrecord("ATA"), Dseqrecord("ATA"), circular=True)
assert not eq(Dseqrecord("ATA"), Dseqrecord("CCC"), circular=True)
assert not eq(Dseqrecord("ATA"), Dseqrecord("ATA"), Dseqrecord("CCC"), circular=True)