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#!/usr/bin/env python
import unittest
from cogent3 import PROTEIN
from cogent3.parse.dialign import DialignParser, parse_data_line
__author__ = "Gavin Huttley"
__copyright__ = "Copyright 2007-2022, The Cogent Project"
__credits__ = ["Gavin Huttley"]
__license__ = "BSD-3"
__version__ = "2023.2.12a1"
__maintainer__ = "Gavin Huttley"
__email__ = "gavin.huttley@anu.edu.au"
__status__ = "Production"
data = """
DIALIGN 2.2.1
*************
Program code written by Burkhard Morgenstern and Said Abdeddaim
e-mail contact: dialign (at) gobics (dot) de
Published research assisted by DIALIGN 2 should cite:
Burkhard Morgenstern (1999).
DIALIGN 2: improvement of the segment-to-segment
approach to multiple sequence alignment.
Bioinformatics 15, 211 - 218.
For more information, please visit the DIALIGN home page at
http://bibiserv.techfak.uni-bielefeld.de/dialign/
************************************************************
program call: dialign -fa -fn /tmp/ct/seq1.fasta /tmp/ct/seq1.txt
Aligned sequences: length:
================== =======
1) HTL2 57
2) MMLV 58
3) HEPB 62
4) ECOL 54
Average seq. length: 57.8
Please note that only upper-case letters are considered to be aligned.
Alignment (DIALIGN format):
===========================
HTL2 1 ldtapC-LFS DGS------P QKAAYVL--- ----WDQTIL QQDITPLPSH
MMLV 1 pdadhtw-YT DGSSLLQEGQ RKAGAAVtte teviWa---- KALDAG---T
HEPB 1 rpgl-CQVFA DAT------P TGWGLVM--- ----GHQRMR GTFSAPLPIH
ECOL 1 mlkqv-EIFT DGSCLGNPGP GGYGAIL--- ----RYRGRE KTFSAGytrT
0000000588 8882222229 9999999000 0000666666 6666633334
HTL2 37 ethSAQKGEL LALICGLRAa k--------- ---
MMLV 43 ---SAQRAEL IALTQALKm- ---------- ---
HEPB 37 t------AEL LAA-CFARSr sganiigtdn svv
ECOL 43 ---TNNRMEL MAAIv----- ---------- ---
0003333455 5533333300 0000000000 000
Sequence tree:
==============
Tree constructed using UPGMAbased on DIALIGN fragment weight scores
((HTL2 :0.130254MMLV :0.130254):0.067788(HEPB :0.120520ECOL :0.120520):0.077521);
""".splitlines()
class TestDialign(unittest.TestCase):
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"
def test_line_split(self):
"""test splitting of sequence record lines"""
result = parse_data_line(
"HTL2 1 ldtapcLFSD GS------PQ KAAYVLWDQT ILQQDITPLP SHethsaqkg "
)
self.assertEqual(
result, ("HTL2", "ldtapcLFSDGS------PQKAAYVLWDQTILQQDITPLPSHethsaqkg")
)
result = parse_data_line(
" 1111111111 1000001111 1111033333 3333333333 3000000000 "
)
self.assertEqual(
result, (None, "11111111111000001111111103333333333333333000000000")
)
def test_aligned_from_dialign(self):
"""test getting aligned seqs"""
aligned_seq = dict(list(DialignParser(data, seq_maker=PROTEIN.make_seq)))
assert aligned_seq == self.aln_seqs
def test_quality_scores(self):
"""test quality scores correctly returned"""
result = dict(
list(DialignParser(data, seq_maker=PROTEIN.make_seq, get_scores=True))
)
assert result["QualityScores"] == self.QualityScores
if __name__ == "__main__":
unittest.main()
|
