def test_pwise_protein(self):
"""works for pairwise protein alignment"""
from cogent3 import PROTEIN
S = make_generic_scoring_dict(1, PROTEIN)
seq1 = PROTEIN.make_seq("MAYPFQLGLQD", "seq1")
seq2 = PROTEIN.make_seq("MAYPFGLQD", "seq2")
a1 = classic_align_pairwise(seq1, seq2, S, 10, 2, local=False)
self.assertEqual(a1.to_dict(),
dict(seq1="MAYPFQLGLQD", seq2="MAYPF--GLQD"))
def setUp(self):
aln_seqs = {
"HTL2": "ldtapC-LFSDGS------PQKAAYVL-------WDQTILQQDITPLPSHethSAQKGELLALICGLRAak------------",
"MMLV": "pdadhtw-YTDGSSLLQEGQRKAGAAVtteteviWa----KALDAG---T---SAQRAELIALTQALKm--------------",
"HEPB": "rpgl-CQVFADAT------PTGWGLVM-------GHQRMRGTFSAPLPIHt------AELLAA-CFARSrsganiigtdnsvv",
"ECOL": "mlkqv-EIFTDGSCLGNPGPGGYGAIL-------RYRGREKTFSAGytrT---TNNRMELMAAIv------------------",
}
self.aln_seqs = {}
for name, seq in list(aln_seqs.items()):
self.aln_seqs[name] = PROTEIN.make_seq(seq, name=name)
self.QualityScores = "00000005888882222229999999900000006666666666633334000333345555333333000000000000000"