Esempi in Python per remove_dots

Esempio n. 1

File: test_Heathpy.py Progetto: hobrien/Python

def test_remove_dots3():
  """test if error handling works correctly when dot in reference seq"""
  align1 = MultipleSeqAlignment([
             SeqRecord(Seq("A.TGCTAGCTAG", generic_dna), id="Alpha"),
             SeqRecord(Seq("ACT-CTAGC.AG", generic_dna), id="Beta"),
             SeqRecord(Seq("ACTGCTAGCTAG", generic_dna), id="Gamma"),
         ])
  remove_dots(align1)

Esempio n. 2

File: test_Heathpy.py Progetto: hobrien/Python

def test_remove_dots():
  aln2 = remove_dots(align1)
  print "testing if %s == ACTGCTAGCTAG" % aln2[0].seq       
  assert str(remove_dots(align1)[0].seq) == "ACTGCTAGCTAG"
  print "testing if %s == ACT-CTAGCTAG" % aln2[1].seq       
  assert str(remove_dots(align1)[1].seq) == "ACT-CTAGCTAG"
  print "testing if %s == ACTGCAAGCTAG" % aln2[2].seq       
  assert str(remove_dots(align1)[2].seq) == "ACTGCAAGCTAG"

Esempio n. 3

File: test_Heathpy.py Progetto: hobrien/Python

def test_remove_dots2():
  """test if sequence names are conserved"""
  aln2 = remove_dots(align1)
  print "testing if %s == Alpha" % aln2[0].id       
  assert aln2[0].id == "Alpha"
  print "testing if %s == Beta" % aln2[1].id       
  assert aln2[1].id == "Beta"
  print "testing if %s == Gamma" % aln2[2].id       
  assert aln2[2].id == "Gamma"