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# Copyright 2012 by Eric Talevich. 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 SeqIO PdbIO module."""
import unittest
import warnings
try:
import numpy
from numpy import dot # Missing on PyPy's micronumpy
del dot
# We don't need this (?) but Bio.PDB imports it automatically :(
from numpy.linalg import svd, det # Missing in PyPy 2.0 numpypy
except ImportError:
from Bio import MissingPythonDependencyError
raise MissingPythonDependencyError(
"Install NumPy if you want to use PDB formats with SeqIO."
) from None
from Bio import SeqIO
from Bio import BiopythonParserWarning
from Bio.PDB.PDBExceptions import PDBConstructionWarning
def SeqresTestGenerator(extension, parser):
"""Test factory for tests reading SEQRES (or similar) records.
This is a factory returning a parameterised superclass for tests reading
sequences from the sequence records of structure files.
Arguments:
extension:
The extension of the files to read from the ``PDB`` directory (e.g.
``pdb`` or ``cif``).
parser:
The name of the SeqIO parser to use (e.g. ``pdb-atom``).
"""
class SeqresTests(unittest.TestCase):
"""Use "parser" to parse sequence records from a structure file.
Args:
parser (str): Name of the parser used by SeqIO.
extension (str): Extension of the files to parse.
"""
def test_seqres_parse(self):
"""Parse a multi-chain PDB by SEQRES entries.
Reference:
http://www.rcsb.org/pdb/files/fasta.txt?structureIdList=2BEG
"""
chains = list(SeqIO.parse("PDB/2BEG." + extension, parser))
self.assertEqual(len(chains), 5)
actual_seq = "DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA"
for chain, chn_id in zip(chains, "ABCDE"):
self.assertEqual(chain.id, "2BEG:" + chn_id)
self.assertEqual(chain.annotations["chain"], chn_id)
self.assertEqual(str(chain.seq), actual_seq)
def test_seqres_read(self):
"""Read a single-chain structure by sequence entries.
Reference:
http://www.rcsb.org/pdb/files/fasta.txt?structureIdList=1A8O
"""
chain = SeqIO.read("PDB/1A8O." + extension, parser)
self.assertEqual(chain.id, "1A8O:A")
self.assertEqual(chain.annotations["chain"], "A")
self.assertEqual(
str(chain.seq),
"MDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPD"
"CKTILKALGPGATLEEMMTACQG",
)
def test_seqres_missing(self):
"""Parse a PDB with no SEQRES entries."""
chains = list(SeqIO.parse("PDB/a_structure." + extension, parser))
self.assertEqual(len(chains), 0)
return SeqresTests
class TestPdbSeqres(SeqresTestGenerator("pdb", "pdb-seqres")):
"""Test pdb-seqres SeqIO driver."""
pass
class TestCifSeqres(SeqresTestGenerator("cif", "cif-seqres")):
"""Test cif-seqres SeqIO driver."""
pass
def AtomTestGenerator(extension, parser):
"""Test factory for tests reading ATOM (or similar) records.
See SeqresTestGenerator for more information.
"""
class AtomTests(unittest.TestCase):
def test_atom_parse(self):
"""Parse a multi-chain structure by ATOM entries.
Reference:
http://www.rcsb.org/pdb/files/fasta.txt?structureIdList=2BEG
"""
chains = list(SeqIO.parse("PDB/2BEG." + extension, parser))
self.assertEqual(len(chains), 5)
actual_seq = "LVFFAEDVGSNKGAIIGLMVGGVVIA"
for chain, chn_id in zip(chains, "ABCDE"):
self.assertEqual(chain.id, "2BEG:" + chn_id)
self.assertEqual(chain.annotations["chain"], chn_id)
self.assertEqual(chain.annotations["model"], 0)
self.assertEqual(str(chain.seq), actual_seq)
with warnings.catch_warnings():
warnings.simplefilter("ignore", PDBConstructionWarning)
chains = list(SeqIO.parse("PDB/2XHE." + extension, parser))
actual_seq = (
"DRLSRLRQMAAENQXXXXXXXXXXXXXXXXXXXXXXXPEPFMADFFNRVK"
"RIRDNIEDIEQAIEQVAQLHTESLVAVSKEDRDRLNEKLQDTMARISALG"
"NKIRADLKQIEKENKRAQQEGTFEDGTVSTDLRIRQSQHSSLSRKFVKVM"
"TRYNDVQAENKRRYGENVARQCRVVEPSLSDDAIQKVIEHGXXXXXXXXX"
"XXXXXXXXNEIRDRHKDIQQLERSLLELHEMFTDMSTLVASQGEMIDRIE"
"FSVEQSHNYV"
)
self.assertEqual(str(chains[1].seq), actual_seq)
def test_atom_read(self):
"""Read a single-chain structure by ATOM entries.
Reference:
http://www.rcsb.org/pdb/files/fasta.txt?structureIdList=1A8O
"""
chain = SeqIO.read("PDB/1A8O." + extension, parser)
self.assertEqual(chain.id, "1A8O:A")
self.assertEqual(chain.annotations["chain"], "A")
self.assertEqual(chain.annotations["model"], 0)
self.assertEqual(
str(chain.seq),
"MDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTIL"
"KALGPGATLEEMMTACQG",
)
return AtomTests
class TestPdbAtom(AtomTestGenerator("pdb", "pdb-atom")):
"""Test pdb-atom SeqIO driver."""
def test_atom_noheader(self):
"""Parse a PDB with no HEADER line."""
with warnings.catch_warnings():
warnings.simplefilter("ignore", PDBConstructionWarning)
warnings.simplefilter("ignore", BiopythonParserWarning)
chains = list(SeqIO.parse("PDB/1LCD.pdb", "pdb-atom"))
self.assertEqual(len(chains), 1)
self.assertEqual(
str(chains[0].seq), "MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNR"
)
def test_atom_read_noheader(self):
"""Read a single-chain PDB without a header by ATOM entries."""
with warnings.catch_warnings():
warnings.simplefilter("ignore", PDBConstructionWarning)
warnings.simplefilter("ignore", BiopythonParserWarning)
chain = SeqIO.read("PDB/a_structure.pdb", "pdb-atom")
self.assertEqual(chain.id, "????:A")
self.assertEqual(chain.annotations["chain"], "A")
self.assertEqual(str(chain.seq), "E")
def test_atom_with_insertion(self):
"""Read a PDB with residue insertion code."""
chain = SeqIO.read("PDB/2n0n_M1.pdb", "pdb-atom")
self.assertEqual(str(chain.seq), "HAEGKFTSEF")
class TestCifAtom(AtomTestGenerator("cif", "cif-atom")):
"""Test cif-atom SeqIO driver."""
def test_atom_read_noheader(self):
"""Read a single-chain CIF without a header by ATOM entries."""
with warnings.catch_warnings():
warnings.simplefilter("ignore", PDBConstructionWarning)
warnings.simplefilter("ignore", BiopythonParserWarning)
chain = SeqIO.read("PDB/a_structure.cif", "cif-atom")
self.assertEqual(chain.id, "????:A")
self.assertEqual(chain.annotations["chain"], "A")
self.assertEqual(
str(chain.seq),
"MDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQG",
)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
|
