"""Testing facility for conkit.io.PconsIO"""
__author__ = "Felix Simkovic"
__date__ = "26 Oct 2016"
import os
import unittest
from conkit.core.contact import Contact
from conkit.core.contactfile import ContactFile
from conkit.core.contactmap import ContactMap
from conkit.core.sequence import Sequence
from conkit.io.tests.helpers import ParserTestCase
from conkit.io.pcons import PconsParser
[docs]class TestPconsParser(ParserTestCase):
[docs] def test_read_1(self):
content = """1 2 0.93514
1 3 0.67324
1 4 0.23692
1 5 0.13166
1 6 0.09188
1 7 0.07957
1 8 0.06556
1 9 0.05188
1 10 0.04146
1 11 0.03264
1 12 0.02515
1 13 0.02137
1 14 0.01961
1 15 0.01710
1 16 0.01397
1 17 0.01192
"""
f_name = self.tempfile(content=content)
with open(f_name, "r") as f_in:
contact_file = PconsParser().read(f_in)
contact_map1 = contact_file.top_map
self.assertEqual(1, len(contact_file))
self.assertEqual(16, len(contact_map1))
self.assertEqual([1] * 16, [c.res1_seq for c in contact_map1])
self.assertEqual(list(range(2, 18)), [c.res2_seq for c in contact_map1])
self.assertEqual([0.93514, 0.67324, 0.23692, 0.13166, 0.09188], [c.raw_score for c in contact_map1][:5])
[docs] def test_read_2(self):
content = """# Check one two
Hello WOrld
1 2 0.93514
1 3 0.67324
1 4 0.23692
1 5 0.13166
1 6 0.09188
1 7 0.07957
1 8 0.06556
1 9 0.05188
1 10 0.04146
1 11 0.03264
1 12 0.02515
1 13 0.02137
1 14 0.01961
1 15 0.01710
1 16 0.01397
1 17 0.01192
"""
f_name = self.tempfile(content=content)
with open(f_name, "r") as f_in:
contact_file = PconsParser().read(f_in)
contact_map1 = contact_file.top_map
self.assertEqual(1, len(contact_file))
self.assertEqual(16, len(contact_map1))
self.assertEqual([1] * 16, [c.res1_seq for c in contact_map1])
self.assertEqual(list(range(2, 18)), [c.res2_seq for c in contact_map1])
self.assertEqual([0.93514, 0.67324, 0.23692, 0.13166, 0.09188], [c.raw_score for c in contact_map1][:5])
[docs] def test_read_3(self):
content = """##############################################################################
PconsC3 result file
Generated from test_remark
Total request time: 83148.0 seconds.
##############################################################################
Sequence number: 1
Sequence name: shorter_test
Sequence length: 33 aa.
Sequence:
HLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSD
Predicted contacts:
Res1 Res2 Score
1 2 0.93514
1 3 0.67324
1 4 0.23692
1 5 0.13166
1 6 0.09188
1 7 0.07957
1 8 0.06556
1 9 0.05188
1 10 0.04146
1 11 0.03264
1 12 0.02515
1 13 0.02137
1 14 0.01961
1 15 0.01710
1 16 0.01397
1 17 0.01192
##############################################################################
"""
f_name = self.tempfile(content=content)
with open(f_name, "r") as f_in:
contact_file = PconsParser().read(f_in)
contact_map1 = contact_file.top_map
self.assertEqual(1, len(contact_file))
self.assertEqual(["Generated from test_remark"], contact_file.remark)
self.assertEqual(16, len(contact_map1))
self.assertEqual([1] * 16, [c.res1_seq for c in contact_map1])
self.assertEqual(list(range(2, 18)), [c.res2_seq for c in contact_map1])
self.assertEqual([0.93514, 0.67324, 0.23692, 0.13166, 0.09188], [c.raw_score for c in contact_map1][:5])
self.assertEqual("shorter_test", contact_map1.sequence.id)
self.assertEqual("HLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSD", contact_map1.sequence.seq)
[docs] def test_read_4(self):
content = """##############################################################################
PconsC3 result file
Generated from test_remark
Total request time: 83148.0 seconds.
##############################################################################
Sequence number: 1
Sequence name: longer_test
Sequence length: 132 aa.
Sequence:
HLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSDHLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSD
HLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSDHLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSD
Predicted contacts:
Res1 Res2 Score
1 2 0.93514
1 3 0.67324
1 4 0.23692
1 5 0.13166
1 6 0.09188
1 7 0.07957
1 8 0.06556
1 9 0.05188
1 10 0.04146
1 11 0.03264
1 12 0.02515
1 13 0.02137
1 14 0.01961
1 15 0.01710
1 16 0.01397
1 17 0.01192
##############################################################################
"""
f_name = self.tempfile(content=content)
with open(f_name, "r") as f_in:
contact_file = PconsParser().read(f_in)
contact_map1 = contact_file.top_map
self.assertEqual(1, len(contact_file))
self.assertEqual(["Generated from test_remark"], contact_file.remark)
self.assertEqual(16, len(contact_map1))
self.assertEqual([1] * 16, [c.res1_seq for c in contact_map1])
self.assertEqual(list(range(2, 18)), [c.res2_seq for c in contact_map1])
self.assertEqual([0.93514, 0.67324, 0.23692, 0.13166, 0.09188], [c.raw_score for c in contact_map1][:5])
self.assertEqual("longer_test", contact_map1.sequence.id)
self.assertEqual(
"HLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSDHLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSD"
"HLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSDHLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSD",
contact_map1.sequence.seq,
)
[docs] def test_write_1(self):
contact_file = ContactFile("RR")
contact_file.target = "R9999"
contact_file.author = "1234-5678-9000"
contact_file.remark = ["Predictor remarks"]
contact_file.method = ["Description of methods used", "Description of methods used"]
contact_map = ContactMap("1")
contact_file.add(contact_map)
for c in [(1, 9, 0, 8, 0.7), (1, 10, 0, 8, 0.7), (2, 8, 0, 8, 0.9), (3, 12, 0, 8, 0.4)]:
contact = Contact(c[0], c[1], c[4], distance_bound=(c[2], c[3]))
contact_map.add(contact)
contact_map.sequence = Sequence("sequence_1", "HLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSD")
contact_map.set_sequence_register()
f_name = self.tempfile()
with open(f_name, "w") as f_out:
PconsParser().write(f_out, contact_file)
content = [
"##############################################################################",
"PconsC3 result file",
"Generated using ConKit",
"##############################################################################",
"Sequence number: 1",
"Sequence name: sequence_1",
"Sequence length: 33 aa.",
"Sequence:",
"HLEGSIGILLKKHEIVFDGCHDFGRTYIWQMSD",
"",
"",
"Predicted contacts:",
"Res1 Res2 Score",
" 1 9 0.700000",
" 1 10 0.700000",
" 2 8 0.900000",
" 3 12 0.400000",
"",
"##############################################################################",
]
with open(f_name, "r") as f_in:
output = f_in.read().splitlines()
self.assertEqual(content, output)
if __name__ == "__main__":
unittest.main(verbosity=2)
