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# Copyright 2003 by Iddo Friedberg. All rights reserved.
# Copyright 2007-2009 by Peter Cock. 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 SeqUtils module."""
import os
import unittest
from Bio import SeqIO
from Bio.Seq import Seq, MutableSeq
from Bio.SeqRecord import SeqRecord
from Bio.SeqUtils import GC, seq1, seq3, GC_skew
from Bio.SeqUtils.lcc import lcc_simp, lcc_mult
from Bio.SeqUtils.CheckSum import crc32, crc64, gcg, seguid
from Bio.SeqUtils.CodonUsage import CodonAdaptationIndex
class SeqUtilsTests(unittest.TestCase):
@classmethod
def setUpClass(cls):
# Example of crc64 collision from Sebastian Bassi using the
# immunoglobulin lambda light chain variable region from Homo sapiens
# Both sequences share the same CRC64 checksum: 44CAAD88706CC153
cls.str_light_chain_one = (
"QSALTQPASVSGSPGQSITISCTGTSSDVGSYNLVSWYQQHPGKAPKLMIYEGSKRPSGV"
"SNRFSGSKSGNTASLTISGLQAEDEADYYCSSYAGSSTLVFGGGTKLTVL"
)
cls.str_light_chain_two = (
"QSALTQPASVSGSPGQSITISCTGTSSDVGSYNLVSWYQQHPGKAPKLMIYEGSKRPSGV"
"SNRFSGSKSGNTASLTISGLQAEDEADYYCCSYAGSSTWVFGGGTKLTVL"
)
X = CodonAdaptationIndex()
path = os.path.join("CodonUsage", "HighlyExpressedGenes.txt")
X.generate_index(path)
cls.X = X
def test_codon_usage_ecoli(self):
"""Test Codon Adaptation Index (CAI) using default E. coli data."""
CAI = CodonAdaptationIndex()
value = CAI.cai_for_gene("ATGCGTATCGATCGCGATACGATTAGGCGGATG")
self.assertAlmostEqual(value, 0.09978, places=5)
def test_codon_usage_custom(self):
"""Test Codon Adaptation Index (CAI) using FASTA file for background."""
# We need a FASTA file of CDS sequences to count the codon usage...
dna_fasta_filename = "fasta.tmp"
dna_genbank_filename = "GenBank/NC_005816.gb"
record = SeqIO.read(dna_genbank_filename, "genbank")
records = []
for feature in record.features:
if feature.type == "CDS" and len(feature.location.parts) == 1:
start = feature.location.start.position
end = feature.location.end.position
table = int(feature.qualifiers["transl_table"][0])
if feature.strand == -1:
seq = record.seq[start:end].reverse_complement()
else:
seq = record.seq[start:end]
# Double check we have the CDS sequence expected
# TODO - Use any cds_start option if/when added to deal with the met
a = "M" + str(seq[3:].translate(table))
b = feature.qualifiers["translation"][0] + "*"
self.assertEqual(a, b, "%r vs %r" % (a, b))
records.append(
SeqRecord(
seq,
id=feature.qualifiers["protein_id"][0],
description=feature.qualifiers["product"][0],
)
)
with open(dna_fasta_filename, "w") as handle:
SeqIO.write(records, handle, "fasta")
CAI = CodonAdaptationIndex()
# Note - this needs a FASTA file which containing non-ambiguous DNA coding
# sequences - which should each be a whole number of codons.
CAI.generate_index(dna_fasta_filename)
# Now check codon usage index (CAI) using this species
self.assertEqual(
record.annotations["source"], "Yersinia pestis biovar Microtus str. 91001"
)
value = CAI.cai_for_gene("ATGCGTATCGATCGCGATACGATTAGGCGGATG")
self.assertAlmostEqual(value, 0.67213, places=5)
os.remove(dna_fasta_filename)
def test_crc_checksum_collision(self):
# Explicit testing of crc64 collision:
self.assertNotEqual(self.str_light_chain_one, self.str_light_chain_two)
self.assertNotEqual(
crc32(self.str_light_chain_one), crc32(self.str_light_chain_two)
)
self.assertEqual(
crc64(self.str_light_chain_one), crc64(self.str_light_chain_two)
)
self.assertNotEqual(
gcg(self.str_light_chain_one), gcg(self.str_light_chain_two)
)
self.assertNotEqual(
seguid(self.str_light_chain_one), seguid(self.str_light_chain_two)
)
def seq_checksums(
self,
seq_str,
exp_crc32,
exp_crc64,
exp_gcg,
exp_seguid,
exp_simple_LCC,
exp_window_LCC,
):
for s in [seq_str, Seq(seq_str), MutableSeq(seq_str)]:
self.assertEqual(exp_crc32, crc32(s))
self.assertEqual(exp_crc64, crc64(s))
self.assertEqual(exp_gcg, gcg(s))
self.assertEqual(exp_seguid, seguid(s))
self.assertAlmostEqual(exp_simple_LCC, lcc_simp(s), places=2)
values = lcc_mult(s, 20)
self.assertEqual(len(exp_window_LCC), len(values))
for value1, value2 in zip(exp_window_LCC, values):
self.assertAlmostEqual(value1, value2, places=2)
def test_checksum1(self):
self.seq_checksums(
self.str_light_chain_one,
2994980265,
"CRC-44CAAD88706CC153",
9729,
"BpBeDdcNUYNsdk46JoJdw7Pd3BI",
1.03,
(
0.00,
1.00,
0.96,
0.96,
0.96,
0.65,
0.43,
0.35,
0.35,
0.35,
0.35,
0.53,
0.59,
0.26,
),
)
def test_checksum2(self):
self.seq_checksums(
self.str_light_chain_two,
802105214,
"CRC-44CAAD88706CC153",
9647,
"X5XEaayob1nZLOc7eVT9qyczarY",
1.07,
(
0.00,
1.00,
0.96,
0.96,
0.96,
0.65,
0.43,
0.35,
0.35,
0.35,
0.35,
0.53,
0.59,
0.26,
),
)
def test_checksum3(self):
self.seq_checksums(
"ATGCGTATCGATCGCGATACGATTAGGCGGAT",
817679856,
"CRC-6234FF451DC6DFC6",
7959,
"8WCUbVjBgiRmM10gfR7XJNjbwnE",
1.98,
(
0.00,
2.00,
1.99,
1.99,
2.00,
1.99,
1.97,
1.99,
1.99,
1.99,
1.96,
1.96,
1.96,
1.96,
),
)
def test_GC(self):
seq = "ACGGGCTACCGTATAGGCAAGAGATGATGCCC"
self.assertEqual(GC(seq), 56.25)
def test_GC_skew(self):
seq = "A" * 50
self.assertEqual(GC_skew(seq)[0], 0)
def test_seq1_seq3(self):
s3 = "MetAlaTyrtrpcysthrLYSLEUILEGlYPrOGlNaSnaLapRoTyRLySSeRHisTrpLysThr"
s1 = "MAYWCTKLIGPQNAPYKSHWKT"
self.assertEqual(seq1(s3), s1)
self.assertEqual(seq3(s1).upper(), s3.upper())
self.assertEqual(seq1(seq3(s1)), s1)
self.assertEqual(seq3(seq1(s3)).upper(), s3.upper())
def test_codon_adaptation_index(self):
X = self.X
cai = X.cai_for_gene(
"ATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGA"
)
self.assertAlmostEqual(cai, 0.6723, places=3)
def test_index(self):
X = self.X
self.assertEqual(len(X.index), 64)
self.assertAlmostEqual(X.index["AAA"], 1.000, places=3)
self.assertAlmostEqual(X.index["AAC"], 1.000, places=3)
self.assertAlmostEqual(X.index["AAG"], 0.219, places=3)
self.assertAlmostEqual(X.index["AAT"], 0.293, places=3)
self.assertAlmostEqual(X.index["ACA"], 0.110, places=3)
self.assertAlmostEqual(X.index["ACC"], 1.000, places=3)
self.assertAlmostEqual(X.index["ACG"], 0.204, places=3)
self.assertAlmostEqual(X.index["ACT"], 0.517, places=3)
self.assertAlmostEqual(X.index["AGA"], 0.018, places=3)
self.assertAlmostEqual(X.index["AGC"], 0.762, places=3)
self.assertAlmostEqual(X.index["AGG"], 0.006, places=3)
self.assertAlmostEqual(X.index["AGT"], 0.195, places=3)
self.assertAlmostEqual(X.index["ATA"], 0.015, places=3)
self.assertAlmostEqual(X.index["ATC"], 1.000, places=3)
self.assertAlmostEqual(X.index["ATG"], 1.000, places=3)
self.assertAlmostEqual(X.index["ATT"], 0.490, places=3)
self.assertAlmostEqual(X.index["CAA"], 0.259, places=3)
self.assertAlmostEqual(X.index["CAC"], 1.000, places=3)
self.assertAlmostEqual(X.index["CAG"], 1.000, places=3)
self.assertAlmostEqual(X.index["CAT"], 0.416, places=3)
self.assertAlmostEqual(X.index["CCA"], 0.247, places=3)
self.assertAlmostEqual(X.index["CCC"], 0.040, places=3)
self.assertAlmostEqual(X.index["CCG"], 1.000, places=3)
self.assertAlmostEqual(X.index["CCT"], 0.161, places=3)
self.assertAlmostEqual(X.index["CGA"], 0.023, places=3)
self.assertAlmostEqual(X.index["CGC"], 0.531, places=3)
self.assertAlmostEqual(X.index["CGG"], 0.014, places=3)
self.assertAlmostEqual(X.index["CGT"], 1.000, places=3)
self.assertAlmostEqual(X.index["CTA"], 0.017, places=3)
self.assertAlmostEqual(X.index["CTC"], 0.100, places=3)
self.assertAlmostEqual(X.index["CTG"], 1.000, places=3)
self.assertAlmostEqual(X.index["CTT"], 0.085, places=3)
self.assertAlmostEqual(X.index["GAA"], 1.000, places=3)
self.assertAlmostEqual(X.index["GAC"], 1.000, places=3)
self.assertAlmostEqual(X.index["GAG"], 0.308, places=3)
self.assertAlmostEqual(X.index["GAT"], 0.886, places=3)
self.assertAlmostEqual(X.index["GCA"], 0.794, places=3)
self.assertAlmostEqual(X.index["GCC"], 0.538, places=3)
self.assertAlmostEqual(X.index["GCG"], 0.937, places=3)
self.assertAlmostEqual(X.index["GCT"], 1.000, places=3)
self.assertAlmostEqual(X.index["GGA"], 0.056, places=3)
self.assertAlmostEqual(X.index["GGC"], 0.892, places=3)
self.assertAlmostEqual(X.index["GGG"], 0.103, places=3)
self.assertAlmostEqual(X.index["GGT"], 1.000, places=3)
self.assertAlmostEqual(X.index["GTA"], 0.465, places=3)
self.assertAlmostEqual(X.index["GTC"], 0.297, places=3)
self.assertAlmostEqual(X.index["GTG"], 0.618, places=3)
self.assertAlmostEqual(X.index["GTT"], 1.000, places=3)
self.assertAlmostEqual(X.index["TAA"], 1.000, places=3)
self.assertAlmostEqual(X.index["TAC"], 1.000, places=3)
self.assertAlmostEqual(X.index["TAG"], 0.012, places=3)
self.assertAlmostEqual(X.index["TAT"], 0.606, places=3)
self.assertAlmostEqual(X.index["TCA"], 0.221, places=3)
self.assertAlmostEqual(X.index["TCC"], 0.785, places=3)
self.assertAlmostEqual(X.index["TCG"], 0.240, places=3)
self.assertAlmostEqual(X.index["TCT"], 1.000, places=3)
self.assertAlmostEqual(X.index["TGA"], 0.081, places=3)
self.assertAlmostEqual(X.index["TGC"], 1.000, places=3)
self.assertAlmostEqual(X.index["TGG"], 1.000, places=3)
self.assertAlmostEqual(X.index["TGT"], 0.721, places=3)
self.assertAlmostEqual(X.index["TTA"], 0.059, places=3)
self.assertAlmostEqual(X.index["TTC"], 1.000, places=3)
self.assertAlmostEqual(X.index["TTG"], 0.072, places=3)
self.assertAlmostEqual(X.index["TTT"], 0.457, places=3)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
|
