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# Copyright 1999 by Jeffrey Chang. 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 SearchIO legacy module."""
import string
import unittest
from io import StringIO
import warnings
from Bio import BiopythonWarning
with warnings.catch_warnings():
warnings.simplefilter("ignore", BiopythonWarning)
from Bio.SearchIO._legacy import ParserSupport
class UndoHandleTests(unittest.TestCase):
"""Tests for the UndoHandle."""
def test_one(self):
"""First test."""
data = """\
This
is
a multi-line
file"""
h = ParserSupport.UndoHandle(StringIO(data))
self.assertEqual(h.readline(), "This\n")
self.assertEqual(h.peekline(), "is\n")
self.assertEqual(h.readline(), "is\n")
# TODO - Meaning of saveline lacking \n?
h.saveline("saved\n")
self.assertEqual(h.peekline(), "saved\n")
h.saveline("another\n")
self.assertEqual(h.readline(), "another\n")
self.assertEqual(h.readline(), "saved\n")
# Test readlines after saveline
h.saveline("saved again\n")
lines = h.readlines()
self.assertEqual(len(lines), 3)
self.assertEqual(lines[0], "saved again\n")
self.assertEqual(lines[1], "a multi-line\n")
self.assertEqual(lines[2], "file") # no trailing \n
# should be empty now
self.assertEqual(h.readline(), "")
h.saveline("save after empty\n")
self.assertEqual(h.readline(), "save after empty\n")
self.assertEqual(h.readline(), "")
def test_read(self):
"""Test read method."""
h = ParserSupport.UndoHandle(StringIO("some text"))
h.saveline("more text")
self.assertEqual(h.read(), "more textsome text")
def test_undohandle_read_block(self):
"""Test reading in blocks."""
data = """\
This
is
a multi-line
file"""
for block in [1, 2, 10]:
s = StringIO(data)
h = ParserSupport.UndoHandle(s)
h.peekline()
new = ""
while True:
tmp = h.read(block)
if not tmp:
break
new += tmp
self.assertEqual(data, new)
h.close()
class TestParserSupport(unittest.TestCase):
def test_TaggingConsumer(self):
h = StringIO()
tc = ParserSupport.TaggingConsumer(handle=h, colwidth=5)
tc.start_section()
self.assertEqual(h.getvalue(), "***** start_section\n")
h.seek(0)
h.truncate(0)
tc.test1("myline")
self.assertEqual(h.getvalue(), "test1: myline\n")
h.seek(0)
h.truncate(0)
tc.end_section()
self.assertEqual(h.getvalue(), "***** end_section\n")
def test_is_blank_line(self):
is_blank_line = ParserSupport.is_blank_line
self.assertTrue(is_blank_line("\n"))
self.assertTrue(is_blank_line("\r\n"))
self.assertTrue(is_blank_line("\r"))
self.assertTrue(is_blank_line(""))
self.assertTrue(is_blank_line("", allow_spaces=1))
self.assertTrue(is_blank_line("", allow_spaces=0))
self.assertTrue(is_blank_line(string.whitespace, allow_spaces=1))
self.assertFalse(is_blank_line("hello"))
self.assertFalse(is_blank_line("hello", allow_spaces=1))
self.assertFalse(is_blank_line("hello", allow_spaces=0))
self.assertFalse(is_blank_line(string.whitespace, allow_spaces=0))
def test_safe_readline(self):
data = """\
This
file"""
h = ParserSupport.UndoHandle(StringIO(data))
safe_readline = ParserSupport.safe_readline
self.assertEqual(safe_readline(h), "This\n")
self.assertEqual(safe_readline(h), "file")
self.assertRaises(ValueError, safe_readline, h)
def test_safe_peekline(self):
safe_peekline = ParserSupport.safe_peekline
data = """\
This
file"""
h = ParserSupport.UndoHandle(StringIO(data))
self.assertEqual(safe_peekline(h), "This\n")
h.readline()
self.assertEqual(safe_peekline(h), "file")
h.readline()
self.assertRaises(ValueError, safe_peekline, h)
h.saveline("hello")
self.assertEqual(safe_peekline(h), "hello")
def test_read_and_call(self):
data = """\
>gi|132871|sp|P19947|RL30_BACSU 50S RIBOSOMAL PROTEIN L30 (BL27)
MAKLEITLKRSVIGRPEDQRVTVRTLGLKKTNQTVVHEDNAAIRGMINKVSHLVSVKEQ
>gi|132679|sp|P19946|RL15_BACSU 50S RIBOSOMAL PROTEIN L15
MKLHELKPSEGSRKTRNRVGRGIGSGNGKTAGKGHKGQNARSGGGVRPGFEGGQMPLFQRLPKRGFTNIN
RKEYAVVNLDKLNGFAEGTEVTPELLLETGVISKLNAGVKILGNGKLEKKLTVKANKFSASAKEAVEAAG
GTAEVI
"""
h = ParserSupport.UndoHandle(StringIO(data))
lines = []
rac = ParserSupport.read_and_call
rac(h, lines.append)
self.assertEqual(lines[-1][:10], ">gi|132871")
rac(h, lines.append, start="MAKLE", end="KEQ", contains="SVIG")
self.assertRaises(ValueError, rac, h, lines.append, blank=1)
self.assertRaises(ValueError, rac, h, lines.append, start="foobar")
self.assertRaises(ValueError, rac, h, lines.append, end="foobar")
self.assertRaises(ValueError, rac, h, lines.append, contains="foobar")
self.assertRaises(ValueError, rac, h, lines.append, blank=0)
def test_attempt_read_and_call(self):
data = """\
>gi|132871|sp|P19947|RL30_BACSU 50S RIBOSOMAL PROTEIN L30 (BL27)
MAKLEITLKRSVIGRPEDQRVTVRTLGLKKTNQTVVHEDNAAIRGMINKVSHLVSVKEQ
>gi|132679|sp|P19946|RL15_BACSU 50S RIBOSOMAL PROTEIN L15
MKLHELKPSEGSRKTRNRVGRGIGSGNGKTAGKGHKGQNARSGGGVRPGFEGGQMPLFQRLPKRGFTNIN
RKEYAVVNLDKLNGFAEGTEVTPELLLETGVISKLNAGVKILGNGKLEKKLTVKANKFSASAKEAVEAAG
GTAEVI"""
h = ParserSupport.UndoHandle(StringIO(data))
lines = []
arac = ParserSupport.attempt_read_and_call
self.assertTrue(arac(h, lines.append, contains="RIBOSOMAL PROTEIN"))
self.assertFalse(arac(h, lines.append, start="foobar"))
self.assertFalse(arac(h, lines.append, blank=1))
self.assertTrue(arac(h, lines.append, end="LVSVKEQ"))
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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