test_module_primer.py

import pytest

def test_primer():
    
    from pydna import primer
    x=primer.Primer("gtatcatatctatctatcta", footprint=12)
    
    assert str(x.seq)  == "gtatcatatctatctatcta"
    assert str(x.tail) == "gtatcata"
    assert str(x.footprint) == "tctatctatcta"
    assert repr(x) == "id 20-mer:5'-gtatcatatctatctatcta-3'"
    assert x.tm() == 41.04993874467033
    
    assert x[0] == "g"
    
    w=x[2:15]
    
    assert repr(w) == "part_id 13-mer:5'-atcatatctatct-3'"
    assert str(w.seq) == 'atcatatctatct'
    
    y ="AAA"+w
    
    assert type(y) == type(w)
    assert str(y.seq) == 'AAAatcatatctatct'
    
    from Bio.Seq import Seq
    from Bio.SeqRecord import SeqRecord
    from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA
    
    arg = "AAA"
    
    a = primer.Primer(arg)
    b = primer.Primer(Seq(arg, IUPACAmbiguousDNA))
    c = primer.Primer(SeqRecord(Seq(arg, IUPACAmbiguousDNA)))
    
    assert str(a.seq) == str(b.seq) == str(c.seq)
    
    assert type(a)==type(b)==type(c)
    
    
    
    #print(str(x.seq).rjust(20))
    #print(str(x.tail))
    #print(str(x.footprint).rjust(20))
    #
    #
    #
    #print(str(w.seq).ljust(20))
    #print(str(w.tail))
    #print(str(w.footprint).rjust(15))



if __name__ == '__main__':
    pytest.main([__file__, "-vv", "-s","--cov=pydna","--cov-report=html"])