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# Copyright 2021 by Michiel de Hoon. All rights reserved.
#
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Tests for Bio.Align.msf module."""
import unittest
import warnings
from Bio import BiopythonParserWarning
from Bio import Align
try:
import numpy
except ImportError:
from Bio import MissingPythonDependencyError
raise MissingPythonDependencyError(
"Install numpy if you want to use Bio.Align.msf."
) from None
class TestMSF(unittest.TestCase):
def test_protein1(self):
path = "msf/W_prot.msf"
alignments = Align.parse(path, "msf")
alignment = next(alignments)
self.assertEqual(len(alignment), 11)
self.assertEqual(alignment.shape, (11, 99))
self.assertEqual(alignment.sequences[0].id, "W*01:01:01:01")
self.assertEqual(alignment.sequences[1].id, "W*01:01:01:02")
self.assertEqual(alignment.sequences[2].id, "W*01:01:01:03")
self.assertEqual(alignment.sequences[3].id, "W*01:01:01:04")
self.assertEqual(alignment.sequences[4].id, "W*01:01:01:05")
self.assertEqual(alignment.sequences[5].id, "W*01:01:01:06")
self.assertEqual(alignment.sequences[6].id, "W*02:01")
self.assertEqual(alignment.sequences[7].id, "W*03:01:01:01")
self.assertEqual(alignment.sequences[8].id, "W*03:01:01:02")
self.assertEqual(alignment.sequences[9].id, "W*04:01")
self.assertEqual(alignment.sequences[10].id, "W*05:01")
self.assertEqual(
alignment.sequences[0].seq,
"GLTPFNGYTAATWTRTAVSSVGMNIPYHGASYLVRNQELRSWTAADKAAQMPWRRNRQSCSKPTCREGGRSGSAKSLRMGRRGCSAQNPKDSHDPPPHL",
)
self.assertEqual(
alignment.sequences[1].seq,
"GLTPFNGYTAATWTRTAVSSVGMNIPYHGASYLVRNQELRSWTAADKAAQMPWRRNRQSCSKPTCREGGRSGSAKSLRMGRRGCSAQNPKDSHDPPPHL",
)
self.assertEqual(
alignment.sequences[2].seq,
"GLTPFNGYTAATWTRTAVSSVGMNIPYHGASYLVRNQELRSWTAADKAAQMPWRRNRQSCSKPTCREGGRSGSAKSLRMGRRGCSAQNPKDSHDPPPHL",
)
self.assertEqual(
alignment.sequences[3].seq,
"GLTPFNGYTAATWTRTAVSSVGMNIPYHGASYLVRNQELRSWTAADKAAQMPWRRNRQSCSKPTCREGGRSGSAKSLRMGRRGCSAQNPKDSHDPPPHL",
)
self.assertEqual(
alignment.sequences[4].seq,
"GLTPFNGYTAATWTRTAVSSVGMNIPYHGASYLVRNQELRSWTAADKAAQMPWRRNRQSCSKPTCREGGRSGSAKSLRMGRRGCSAQNPKDSHDPPPHL",
)
self.assertEqual(
alignment.sequences[5].seq,
"GLTPFNGYTAATWTRTAVSSVGMNIPYHGASYLVRNQELRSWTAADKAAQMPWRRNRQSCSKPTCREGGRSGSAKSLRMGRRGCSAQNPKDSHDPPPHL",
)
self.assertEqual(
alignment.sequences[6].seq,
"GLTPSNGYTAATWTRTAASSVGMNIPYDGASYLVRNQELRSWTAADKAAQMPWRRNMQSCSKPTCREGGRSGSAKSLRMGRRRCTAQNPKRLT",
)
self.assertEqual(
alignment.sequences[7].seq,
"GLTPSSGYTAATWTRTAVSSVGMNIPYHGASYLVRNQELRSWTAADKAAQMPWRRNRQSCSKPTCREGGRSGSAKSLRMGRRGCSAQNPKRLT",
)
self.assertEqual(
alignment.sequences[8].seq,
"GLTPSSGYTAATWTRTAVSSVGMNIPYHGASYLVRNQELRSWTAADKAAQMPWRRNRQSCSKPTCREGGRSGSAKSLRMGRRGCSAQNPKRLT",
)
self.assertEqual(
alignment.sequences[9].seq,
"GLTPSNGYTAATWTRTAASSVGMNIPYDGASYLVRNQELRSWTAADKAAQMPWRRNMQSCSKPTCREGGRSGSAKSLRMGRRGCSAQNPKRLT",
)
self.assertEqual(
alignment.sequences[10].seq,
"GLTPSSGYTAATWTRTAVSSVGMNIPYHGASYLVRNQELRSWTAADKAAQMPWRRNRQSCSKPTCREGGRSGSAKSLRMGRRGCSAQNPKDSHDPPPHL",
)
self.assertTrue(
numpy.array_equal(
alignment.coordinates,
numpy.array(
[
[0, 93, 99],
[0, 93, 99],
[0, 93, 99],
[0, 93, 99],
[0, 93, 99],
[0, 93, 99],
[0, 93, 93],
[0, 93, 93],
[0, 93, 93],
[0, 93, 93],
[0, 93, 99],
]
),
)
)
self.assertEqual(
alignment[0],
"GLTPFNGYTAATWTRTAVSSVGMNIPYHGASYLVRNQELRSWTAADKAAQMPWRRNRQSCSKPTCREGGRSGSAKSLRMGRRGCSAQNPKDSHDPPPHL",
)
self.assertEqual(
alignment[1],
"GLTPFNGYTAATWTRTAVSSVGMNIPYHGASYLVRNQELRSWTAADKAAQMPWRRNRQSCSKPTCREGGRSGSAKSLRMGRRGCSAQNPKDSHDPPPHL",
)
self.assertEqual(
alignment[2],
"GLTPFNGYTAATWTRTAVSSVGMNIPYHGASYLVRNQELRSWTAADKAAQMPWRRNRQSCSKPTCREGGRSGSAKSLRMGRRGCSAQNPKDSHDPPPHL",
)
self.assertEqual(
alignment[3],
"GLTPFNGYTAATWTRTAVSSVGMNIPYHGASYLVRNQELRSWTAADKAAQMPWRRNRQSCSKPTCREGGRSGSAKSLRMGRRGCSAQNPKDSHDPPPHL",
)
self.assertEqual(
alignment[4],
"GLTPFNGYTAATWTRTAVSSVGMNIPYHGASYLVRNQELRSWTAADKAAQMPWRRNRQSCSKPTCREGGRSGSAKSLRMGRRGCSAQNPKDSHDPPPHL",
)
self.assertEqual(
alignment[5],
"GLTPFNGYTAATWTRTAVSSVGMNIPYHGASYLVRNQELRSWTAADKAAQMPWRRNRQSCSKPTCREGGRSGSAKSLRMGRRGCSAQNPKDSHDPPPHL",
)
self.assertEqual(
alignment[6],
"GLTPSNGYTAATWTRTAASSVGMNIPYDGASYLVRNQELRSWTAADKAAQMPWRRNMQSCSKPTCREGGRSGSAKSLRMGRRRCTAQNPKRLT------",
)
self.assertEqual(
alignment[7],
"GLTPSSGYTAATWTRTAVSSVGMNIPYHGASYLVRNQELRSWTAADKAAQMPWRRNRQSCSKPTCREGGRSGSAKSLRMGRRGCSAQNPKRLT------",
)
self.assertEqual(
alignment[8],
"GLTPSSGYTAATWTRTAVSSVGMNIPYHGASYLVRNQELRSWTAADKAAQMPWRRNRQSCSKPTCREGGRSGSAKSLRMGRRGCSAQNPKRLT------",
)
self.assertEqual(
alignment[9],
"GLTPSNGYTAATWTRTAASSVGMNIPYDGASYLVRNQELRSWTAADKAAQMPWRRNMQSCSKPTCREGGRSGSAKSLRMGRRGCSAQNPKRLT------",
)
self.assertEqual(
alignment[10],
"GLTPSSGYTAATWTRTAVSSVGMNIPYHGASYLVRNQELRSWTAADKAAQMPWRRNRQSCSKPTCREGGRSGSAKSLRMGRRGCSAQNPKDSHDPPPHL",
)
with self.assertRaises(StopIteration):
next(alignments)
def test_protein2(self):
path = "msf/DOA_prot.msf"
alignments = Align.parse(path, "msf")
with warnings.catch_warnings(record=True) as w:
alignment = next(alignments)
self.assertEqual(len(w), 1)
self.assertIsInstance(w[0].message, BiopythonParserWarning)
self.assertEqual(
str(w[0].message), "GCG MSF headers said alignment length 62, but found 250"
)
self.assertEqual(len(alignment), 12)
self.assertEqual(alignment.shape, (12, 250))
self.assertEqual(alignment.sequences[0].id, "DOA*01:01:01")
self.assertEqual(alignment.sequences[1].id, "DOA*01:01:02:01")
self.assertEqual(alignment.sequences[2].id, "DOA*01:01:02:02")
self.assertEqual(alignment.sequences[3].id, "DOA*01:01:02:03")
self.assertEqual(alignment.sequences[4].id, "DOA*01:01:03")
self.assertEqual(alignment.sequences[5].id, "DOA*01:01:04:01")
self.assertEqual(alignment.sequences[6].id, "DOA*01:01:04:02")
self.assertEqual(alignment.sequences[7].id, "DOA*01:01:05")
self.assertEqual(alignment.sequences[8].id, "DOA*01:01:06")
self.assertEqual(alignment.sequences[9].id, "DOA*01:02")
self.assertEqual(alignment.sequences[10].id, "DOA*01:03")
self.assertEqual(alignment.sequences[11].id, "DOA*01:04N")
self.assertEqual(
alignment.sequences[0].seq,
"MALRAGLVLGFHTLMTLLSPQEAGATKADHMGSYGPAFYQSYGASGQFTHEFDEEQLFSVDLKKSEAVWRLPEFGDFARFDPQGGLAGIAAIKAHLDILVERSNRSRAINVPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQVEHWGLDAPLLRHWELQVPIPPPDAMETLVCALGLAIGLVGFLVGTVLIIMGTYVSSVPR",
)
self.assertEqual(
alignment.sequences[1].seq,
"MALRAGLVLGFHTLMTLLSPQEAGATKADHMGSYGPAFYQSYGASGQFTHEFDEEQLFSVDLKKSEAVWRLPEFGDFARFDPQGGLAGIAAIKAHLDILVERSNRSRAINVPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQVEHWGLDAPLLRHWELQVPIPPPDAMETLVCALGLAIGLVGFLVGTVLIIMGTYVSSVPR",
)
self.assertEqual(
alignment.sequences[2].seq,
"MALRAGLVLGFHTLMTLLSPQEAGATKADHMGSYGPAFYQSYGASGQFTHEFDEEQLFSVDLKKSEAVWRLPEFGDFARFDPQGGLAGIAAIKAHLDILVERSNRSRAINVPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQVEHWGLDAPLLRHWELQVPIPPPDAMETLVCALGLAIGLVGFLVGTVLIIMGTYVSSVPR",
)
self.assertEqual(
alignment.sequences[3].seq,
"MALRAGLVLGFHTLMTLLSPQEAGATKADHMGSYGPAFYQSYGASGQFTHEFDEEQLFSVDLKKSEAVWRLPEFGDFARFDPQGGLAGIAAIKAHLDILVERSNRSRAINVPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQVEHWGLDAPLLRHWELQVPIPPPDAMETLVCALGLAIGLVGFLVGTVLIIMGTYVSSVPR",
)
self.assertEqual(
alignment.sequences[4].seq,
"DHMGSYGPAFYQSYGASGQFTHEFDEEQLFSVDLKKSEAVWRLPEFGDFARFDPQGGLAGIAAIKAHLDILVERSNRSRAINVPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQVEHWGLDAPLLRHWELQVPIPPPDAMETLVCALGLAIGLVGFLVGTVLIIMGTYVSSVPR",
)
self.assertEqual(
alignment.sequences[5].seq,
"MALRAGLVLGFHTLMTLLSPQEAGATKADHMGSYGPAFYQSYGASGQFTHEFDEEQLFSVDLKKSEAVWRLPEFGDFARFDPQGGLAGIAAIKAHLDILVERSNRSRAINVPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQVEHWGLDAPLLRHWELQVPIPPPDAMETLVCALGLAIGLVGFLVGTVLIIMGTYVSSVPR",
)
self.assertEqual(
alignment.sequences[6].seq,
"DHMGSYGPAFYQSYGASGQFTHEFDEEQLFSVDLKKSEAVWRLPEFGDFARFDPQGGLAGIAAIKAHLDILVERSNRSRAINVPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQVEHWGLDAPLLRHWELQVPIPPPDAMETLVCALGLAIGLVGFLVGTVLIIMGTYVSSVPR",
)
self.assertEqual(
alignment.sequences[7].seq,
"MALRAGLVLGFHTLMTLLSPQEAGATKADHMGSYGPAFYQSYGASGQFTHEFDEEQLFSVDLKKSEAVWRLPEFGDFARFDPQGGLAGIAAIKAHLDILVERSNRSRAINVPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQVEHWGLDAPLLRHWELQVPIPPPDAMETLVCALGLAIGLVGFLVGTVLIIMGTYVSSVPR",
)
self.assertEqual(
alignment.sequences[8].seq,
"MALRAGLVLGFHTLMTLLSPQEAGATKADHMGSYGPAFYQSYGASGQFTHEFDEEQLFSVDLKKSEAVWRLPEFGDFARFDPQGGLAGIAAIKAHLDILVERSNRSRAINVPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQVEHWGLDAPLLRHWELQVPIPPPDAMETLVCALGLAIGLVGFLVGTVLIIMGTYVSSVPR",
)
self.assertEqual(
alignment.sequences[9].seq,
"MALRAGLVLGFHTLMTLLSPQEAGATKADHMGSYGPAFYQSYGASGQFTHEFDEEQLFSVDLKKSEAVWRLPEFGDFARFDPQGGLAGIAAIKAHLDILVERSNCSRAINVPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQVEHWGLDAPLLRHWELQVPIPPPDAMETLVCALGLAIGLVGFLVGTVLIIMGTYVSSVPR",
)
self.assertEqual(
alignment.sequences[10].seq,
"MALRAGLVLGFHTLMTLLSPQEAGATKADHMGSYGPAFYQSYGASGQFTHEFDEEQLFSVDLKKSEAVWRLPEFGDFARFDPQGGLAGIAAIKAHLDIVVERSNRSRAINVPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQVEHWGLDAPLLRHWELQVPIPPPDAMETLVCALGLAIGLVGFLVGTVLIIMGTYVSSVPR",
)
self.assertEqual(
alignment.sequences[11].seq,
"MALRAGLVLGFHTLMTLLSPQEAGATKADHMGSYGPPSTSLTAPRASSPMNLMRNSCSLWTX",
)
self.assertTrue(
numpy.array_equal(
alignment.coordinates,
numpy.array(
[
[0, 28, 62, 250],
[0, 28, 62, 250],
[0, 28, 62, 250],
[0, 28, 62, 250],
[0, 0, 34, 222],
[0, 28, 62, 250],
[0, 0, 34, 222],
[0, 28, 62, 250],
[0, 28, 62, 250],
[0, 28, 62, 250],
[0, 28, 62, 250],
[0, 28, 62, 62],
],
),
)
)
self.assertEqual(
alignment[0],
"MALRAGLVLGFHTLMTLLSPQEAGATKADHMGSYGPAFYQSYGASGQFTHEFDEEQLFSVDLKKSEAVWRLPEFGDFARFDPQGGLAGIAAIKAHLDILVERSNRSRAINVPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQVEHWGLDAPLLRHWELQVPIPPPDAMETLVCALGLAIGLVGFLVGTVLIIMGTYVSSVPR",
)
self.assertEqual(
alignment[1],
"MALRAGLVLGFHTLMTLLSPQEAGATKADHMGSYGPAFYQSYGASGQFTHEFDEEQLFSVDLKKSEAVWRLPEFGDFARFDPQGGLAGIAAIKAHLDILVERSNRSRAINVPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQVEHWGLDAPLLRHWELQVPIPPPDAMETLVCALGLAIGLVGFLVGTVLIIMGTYVSSVPR",
)
self.assertEqual(
alignment[2],
"MALRAGLVLGFHTLMTLLSPQEAGATKADHMGSYGPAFYQSYGASGQFTHEFDEEQLFSVDLKKSEAVWRLPEFGDFARFDPQGGLAGIAAIKAHLDILVERSNRSRAINVPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQVEHWGLDAPLLRHWELQVPIPPPDAMETLVCALGLAIGLVGFLVGTVLIIMGTYVSSVPR",
)
self.assertEqual(
alignment[3],
"MALRAGLVLGFHTLMTLLSPQEAGATKADHMGSYGPAFYQSYGASGQFTHEFDEEQLFSVDLKKSEAVWRLPEFGDFARFDPQGGLAGIAAIKAHLDILVERSNRSRAINVPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQVEHWGLDAPLLRHWELQVPIPPPDAMETLVCALGLAIGLVGFLVGTVLIIMGTYVSSVPR",
)
self.assertEqual(
alignment[4],
"----------------------------DHMGSYGPAFYQSYGASGQFTHEFDEEQLFSVDLKKSEAVWRLPEFGDFARFDPQGGLAGIAAIKAHLDILVERSNRSRAINVPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQVEHWGLDAPLLRHWELQVPIPPPDAMETLVCALGLAIGLVGFLVGTVLIIMGTYVSSVPR",
)
self.assertEqual(
alignment[5],
"MALRAGLVLGFHTLMTLLSPQEAGATKADHMGSYGPAFYQSYGASGQFTHEFDEEQLFSVDLKKSEAVWRLPEFGDFARFDPQGGLAGIAAIKAHLDILVERSNRSRAINVPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQVEHWGLDAPLLRHWELQVPIPPPDAMETLVCALGLAIGLVGFLVGTVLIIMGTYVSSVPR",
)
self.assertEqual(
alignment[6],
"----------------------------DHMGSYGPAFYQSYGASGQFTHEFDEEQLFSVDLKKSEAVWRLPEFGDFARFDPQGGLAGIAAIKAHLDILVERSNRSRAINVPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQVEHWGLDAPLLRHWELQVPIPPPDAMETLVCALGLAIGLVGFLVGTVLIIMGTYVSSVPR",
)
self.assertEqual(
alignment[7],
"MALRAGLVLGFHTLMTLLSPQEAGATKADHMGSYGPAFYQSYGASGQFTHEFDEEQLFSVDLKKSEAVWRLPEFGDFARFDPQGGLAGIAAIKAHLDILVERSNRSRAINVPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQVEHWGLDAPLLRHWELQVPIPPPDAMETLVCALGLAIGLVGFLVGTVLIIMGTYVSSVPR",
)
self.assertEqual(
alignment[8],
"MALRAGLVLGFHTLMTLLSPQEAGATKADHMGSYGPAFYQSYGASGQFTHEFDEEQLFSVDLKKSEAVWRLPEFGDFARFDPQGGLAGIAAIKAHLDILVERSNRSRAINVPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQVEHWGLDAPLLRHWELQVPIPPPDAMETLVCALGLAIGLVGFLVGTVLIIMGTYVSSVPR",
)
self.assertEqual(
alignment[9],
"MALRAGLVLGFHTLMTLLSPQEAGATKADHMGSYGPAFYQSYGASGQFTHEFDEEQLFSVDLKKSEAVWRLPEFGDFARFDPQGGLAGIAAIKAHLDILVERSNCSRAINVPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQVEHWGLDAPLLRHWELQVPIPPPDAMETLVCALGLAIGLVGFLVGTVLIIMGTYVSSVPR",
)
self.assertEqual(
alignment[10],
"MALRAGLVLGFHTLMTLLSPQEAGATKADHMGSYGPAFYQSYGASGQFTHEFDEEQLFSVDLKKSEAVWRLPEFGDFARFDPQGGLAGIAAIKAHLDIVVERSNRSRAINVPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQVEHWGLDAPLLRHWELQVPIPPPDAMETLVCALGLAIGLVGFLVGTVLIIMGTYVSSVPR",
)
self.assertEqual(
alignment[11],
"MALRAGLVLGFHTLMTLLSPQEAGATKADHMGSYGPPSTSLTAPRASSPMNLMRNSCSLWTX--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------",
)
with self.assertRaises(StopIteration):
next(alignments)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
|
