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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.
import os
import sys
import unittest
from types import *
from Bio import Fasta
from Bio import SeqRecord
from Bio import Seq
from Bio import Alphabet
from Bio.Alphabet import IUPAC
def run_tests(argv):
test_suite = testing_suite()
runner = unittest.TextTestRunner(sys.stdout, verbosity = 2)
runner.run(test_suite)
def testing_suite():
"""Generate the suite of tests.
"""
test_suite = unittest.TestSuite()
test_loader = unittest.TestLoader()
test_loader.testMethodPrefix = 't_'
tests = [RecordTest, ParserTest, IteratorTest]
for test in tests:
cur_suite = test_loader.loadTestsFromTestCase(test)
test_suite.addTest(cur_suite)
return test_suite
class RecordTest(unittest.TestCase):
def t_record_basic(self):
"""Basic test on Record
"""
def pbool(b):
if b:
return 1
return 0
r = Fasta.Record()
assert pbool(type(r.title) is StringType) # StringType
assert pbool(type(r.sequence) is StringType) # StringType
class ParserTest(unittest.TestCase):
def setUp(self):
files = ["f001", "f002"]
self.handles = []
for filename in files:
self.handles.append(open(os.path.join("Fasta", filename)))
self.lengths = {0 : (96, 79),
1 : (100, 633)}
def tearDown(self):
for handle in self.handles:
handle.close()
def t_record_parser(self):
"""Basic operation of the Record Parser.
"""
parser = Fasta.RecordParser()
for index in range(len(self.handles)):
handle = self.handles[index]
rec = parser.parse(handle)
assert isinstance(rec, Fasta.Record)
assert len(rec.title) == self.lengths[index][0]
assert len(rec.sequence) == self.lengths[index][1]
def t_sequence_parser(self):
"""Basic operation of the Sequence Parser.
"""
parser = Fasta.SequenceParser()
for index in range(len(self.handles)):
handle = self.handles[index]
rec = parser.parse(handle)
assert isinstance(rec, SeqRecord.SeqRecord)
assert isinstance(rec.seq, Seq.Seq)
assert rec.seq.alphabet == Alphabet.generic_alphabet
assert len(rec.seq) == self.lengths[index][1]
assert len(rec.description) == self.lengths[index][0]
def t_sequence_alphabet(self):
"""Setting the alphabet for the Sequence Parser.
"""
parser = Fasta.SequenceParser(alphabet =
IUPAC.unambiguous_dna)
rec = parser.parse(self.handles[0])
assert rec.seq.alphabet == IUPAC.unambiguous_dna
def t_sequence_title_convert(self):
"""Test title conversion for the Sequence Parser.
"""
def test_title2ids(title):
return "id", "name", "description"
parser = Fasta.SequenceParser(title2ids = test_title2ids)
rec = parser.parse(self.handles[0])
assert rec.id == "id"
assert rec.name == "name"
assert rec.description == "description"
class IteratorTest(unittest.TestCase):
def setUp(self):
self.test_handle = open(os.path.join('Fasta', 'f002'))
def tearDown(self):
self.test_handle.close()
def t_basic_iterator(self):
"""Ensure the Fasta iterator works returning text.
"""
i = Fasta.Iterator(self.test_handle)
rec_info = {0 : ">gi|1348912|gb|G26680|G26680",
1 : ">gi|1348917|gb|G26685|G26685",
2 : ">gi|1592936|gb|G29385|G29385"}
for rec_num in range(3):
rec = i.next()
lines = rec.split("\n")
title_part = lines[0].split()
assert title_part[0] == rec_info[rec_num]
# make sure we keep getting None when the iterator is done
assert i.next() is None
assert i.next() is None
def t_new_iterator(self):
"""Ensure the Fasta iterator works like a Python 2.2 iterator.
"""
n = 0
iterator = Fasta.Iterator(self.test_handle)
for rec in iter(iterator):
n += 1
assert n == 3
def t_record_iterator(self):
"""Test the iterator with a Record Parser.
"""
parser = Fasta.RecordParser()
iterator = Fasta.Iterator(self.test_handle, parser)
for rec in iter(iterator):
assert isinstance(rec, Fasta.Record)
def t_sequence_iterator(self):
"""Test the iterator with a Sequence Parser.
"""
parser = Fasta.SequenceParser()
iterator = Fasta.Iterator(self.test_handle, parser)
for rec in iter(iterator):
assert isinstance(rec, SeqRecord.SeqRecord)
def t_parsing_comments(self):
"""Parse FASTA files with # style comment lines in them.
"""
handle = open(os.path.join("Fasta", "f003"))
iterator = Fasta.Iterator(handle, Fasta.RecordParser())
num_recs = 0
for rec in iter(iterator):
num_recs += 1
assert num_recs == 2
##The dictionaries code has been deprecated
#class DictionaryTest(unittest.TestCase):
# ...
if __name__ == "__main__":
sys.exit(run_tests(sys.argv))
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