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# Copyright 2015 by Kai Blin.
# 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.
import unittest
import warnings
from os import path
from Bio import SeqIO
from Bio import BiopythonParserWarning
class EMBLTests(unittest.TestCase):
def test_embl_content_after_co(self):
"""Test a ValueError is thrown by content after a CO line"""
def parse_content_after_co():
rec = SeqIO.read(path.join('EMBL', 'xx_after_co.embl'), 'embl')
self.assertRaises(ValueError, parse_content_after_co)
try:
parse_content_after_co()
except ValueError as e:
self.assertEqual(str(e), "Unexpected content after SQ or CO line: 'XX'")
else:
self.assertTrue(False, "Error message without explanation raised by content after CO line")
def test_embl_0_line(self):
"""Test SQ line with 0 length sequence"""
# Biopython 1.67 and older would parse this file with a warning:
# 'Expected sequence length 1740, found 1744 (TIR43YW1_CE).' and
# the coordinates 1740 added to the sequence as four extra letters.
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
rec = SeqIO.read('EMBL/embl_with_0_line.embl', 'embl')
self.assertEqual(len(w), 0, "Unexpected parser warnings: " +
"\n".join(str(warn.message) for warn in w))
self.assertEqual(len(rec), 1740)
def test_embl_no_coords(self):
"""Test sequence lines without coordinates."""
# Biopython 1.68, 1.69 and 1.70 would ignore these lines
# giving an unknown sequence!
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always", BiopythonParserWarning)
rec = SeqIO.read('EMBL/101ma_no_coords.embl', 'embl')
self.assertTrue(w, "Expected parser warning")
self.assertEqual([str(_.message) for _ in w],
["EMBL sequence line missing coordinates"] * 3)
self.assertEqual(len(rec), 154)
self.assertEqual(rec.seq[:10], "MVLSEGEWQL")
self.assertEqual(rec.seq[-10:], "AKYKELGYQG")
def test_embl_wrong_dr_line(self):
"""Test files with wrong DR lines"""
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always", BiopythonParserWarning)
record = SeqIO.read('EMBL/RepBase23.02.embl', 'embl')
self.assertTrue(w, "Expected parser warning")
self.assertEqual([str(_.message) for _ in w],
["Malformed DR line in EMBL file."])
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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