Python eq Examples

Example #1

File: test_module_dseq.py Project: joskid/pydna

 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)

Example #2

File: test_module_utils.py Project: KBRI-Biology-Experiment-Simulation/pydna

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)