test_Restriction.py

# 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.
#

"""Testing code for Restriction enzyme classes of Biopython."""

from Bio.Restriction import Analysis, Restriction, RestrictionBatch
from Bio.Restriction import CommOnly, NonComm, AllEnzymes
from Bio.Restriction import (Acc65I, Asp718I, BamHI, EcoRI, EcoRV, KpnI, SmaI,
                             MluCI, McrI, NdeI, BsmBI, AanI, EarI, SnaI, SphI)
from Bio.Restriction import FormattedSeq
from Bio.Seq import Seq, MutableSeq
from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA
from Bio import BiopythonWarning


from sys import version_info
if version_info[0] < 3:
    try:
        import unittest2 as unittest
    except ImportError:
        from Bio import MissingPythonDependencyError
        raise MissingPythonDependencyError("Under Python 2 this test needs "
                                           "the unittest2 library")
else:
    import unittest


class SequenceTesting(unittest.TestCase):
    """Tests for dealing with input."""

    def test_sequence_object(self):
        """Test if sequence must be a Seq or MutableSeq object."""
        with self.assertRaises(TypeError):
            seq = FormattedSeq('GATC')
        seq = FormattedSeq(Seq('TAGC'))
        seq = FormattedSeq(MutableSeq('AGTC'))
        seq = FormattedSeq(seq)
        with self.assertRaises(TypeError):
            EcoRI.search('GATC')
        EcoRI.search(Seq('ATGC'))
        EcoRI.search(MutableSeq('TCAG'))

    def test_non_iupac_letters(self):
        """Test if non-IUPAC letters raise a TypeError."""
        with self.assertRaises(TypeError):
            seq = FormattedSeq(Seq('GATCZ'))

    def test_formatted_seq(self):
        """Test several methods of FormattedSeq."""
        self.assertEqual(str(FormattedSeq(Seq('GATC'))),
                         "FormattedSeq(Seq('GATC'), linear=True)")
        self.assertFalse(FormattedSeq(Seq('GATC')) ==
                         FormattedSeq(Seq('TAGC')))
        self.assertFalse(FormattedSeq(Seq('TAGC')) == Seq('TAGC'))
        self.assertTrue(FormattedSeq(Seq('ATGC')) ==
                        FormattedSeq(Seq('ATGC')))
        linear_seq = FormattedSeq(Seq('T'))
        self.assertTrue(linear_seq.is_linear())
        linear_seq.circularise()
        self.assertFalse(linear_seq.is_linear())
        linear_seq.linearise()
        circular_seq = linear_seq.to_circular()
        self.assertFalse(circular_seq.is_linear())
        linear_seq = circular_seq.to_linear()
        self.assertTrue(linear_seq.is_linear())


class SimpleEnzyme(unittest.TestCase):
    """Tests for dealing with basic enzymes using the Restriction package."""

    def test_init(self):
        """Check for error during __init__."""
        with self.assertRaises(ValueError) as ve:
            Restriction.OneCut('bla-me', (Restriction.RestrictionType,),
                               dict())
            self.assertIn('hyphen', str(ve.exception))

    def setUp(self):
        """Set up some sequences for later use."""
        base_seq = Seq("AAAA", IUPACAmbiguousDNA())
        self.ecosite_seq = base_seq + Seq(EcoRI.site,
                                          IUPACAmbiguousDNA()) + base_seq
        self.smasite_seq = base_seq + Seq(SmaI.site,
                                          IUPACAmbiguousDNA()) + base_seq
        self.kpnsite_seq = base_seq + Seq(KpnI.site,
                                          IUPACAmbiguousDNA()) + base_seq

    def test_eco_cutting(self):
        """Test basic cutting with EcoRI (5'overhang)."""
        self.assertEqual(EcoRI.site, 'GAATTC')
        self.assertTrue(EcoRI.cut_once())
        self.assertFalse(EcoRI.is_blunt())
        self.assertTrue(EcoRI.is_5overhang())
        self.assertFalse(EcoRI.is_3overhang())
        self.assertEqual(EcoRI.overhang(), "5' overhang")
        self.assertTrue(EcoRI.is_defined())
        self.assertFalse(EcoRI.is_ambiguous())
        self.assertFalse(EcoRI.is_unknown())
        self.assertTrue(EcoRI.is_palindromic())
        self.assertTrue(EcoRI.is_comm())
        self.assertIn('Life Technologies', EcoRI.supplier_list())
        self.assertEqual(EcoRI.elucidate(), "G^AATT_C")
        self.assertEqual(EcoRI.search(self.ecosite_seq), [6])
        self.assertEqual(EcoRI.characteristic(), (1, -1, None, None, 'GAATTC'))

        parts = EcoRI.catalyse(self.ecosite_seq)
        self.assertEqual(len(parts), 2)
        self.assertEqual(str(parts[1]), "AATTCAAAA")
        parts = EcoRI.catalyze(self.ecosite_seq)
        self.assertEqual(len(parts), 2)

    def test_kpn_cutting(self):
        """Test basic cutting with KpnI (3'overhang)."""
        self.assertTrue(KpnI.is_3overhang())
        self.assertFalse(KpnI.is_5overhang())
        self.assertFalse(KpnI.is_blunt())
        self.assertEqual(KpnI.overhang(), "3' overhang")
        parts = KpnI.catalyse(self.kpnsite_seq)
        self.assertEqual(len(parts), 2)
        self.assertEqual(KpnI.catalyse(self.kpnsite_seq),
                         KpnI.catalyze(self.kpnsite_seq))

    def test_sma_cutting(self):
        """Test basic cutting with SmaI (blunt cutter)."""
        self.assertTrue(SmaI.is_blunt())
        self.assertFalse(SmaI.is_3overhang())
        self.assertFalse(SmaI.is_5overhang())
        self.assertEqual(SmaI.overhang(), 'blunt')
        parts = SmaI.catalyse(self.smasite_seq)
        self.assertEqual(len(parts), 2)
        self.assertEqual(str(parts[1]), "GGGAAAA")
        parts = SmaI.catalyze(self.smasite_seq)
        self.assertEqual(len(parts), 2)

    def test_ear_cutting(self):
        """Test basic cutting with EarI (ambiguous overhang)."""
        self.assertFalse(EarI.is_palindromic())
        self.assertFalse(EarI.is_defined())
        self.assertTrue(EarI.is_ambiguous())
        self.assertFalse(EarI.is_unknown())
        self.assertEqual(EarI.elucidate(), 'CTCTTCN^NNN_N')

    def test_sna_cutting(self):
        """Test basic cutting with SnaI (unknown)."""
        self.assertEqual(SnaI.elucidate(), '? GTATAC ?')
        self.assertFalse(SnaI.is_defined())
        self.assertFalse(SnaI.is_ambiguous())
        self.assertTrue(SnaI.is_unknown())
        self.assertFalse(SnaI.is_comm())
        self.assertEqual(SnaI.suppliers(), None)
        self.assertEqual(SnaI.supplier_list(), [])
        with self.assertRaises(TypeError):
            SnaI.buffers('no company')

    def test_circular_sequences(self):
        """Deal with cutting circular sequences."""
        parts = EcoRI.catalyse(self.ecosite_seq, linear=False)
        self.assertEqual(len(parts), 1)
        locations = EcoRI.search(parts[0], linear=False)
        self.assertEqual(locations, [1])

        parts = KpnI.catalyse(self.kpnsite_seq, linear=False)
        self.assertEqual(len(parts), 1)
        locations = KpnI.search(parts[0], linear=False)
        self.assertEqual(locations, [1])

        parts = SmaI.catalyse(self.smasite_seq, linear=False)
        self.assertEqual(len(parts), 1)
        locations = SmaI.search(parts[0], linear=False)
        self.assertEqual(locations, [1])

        self.assertEqual(EarI.search(FormattedSeq(Seq('CTCTTCAAAAA')),
                                     linear=False), [8])
        self.assertEqual(SnaI.search(FormattedSeq(Seq('GTATACAAAAA')),
                                     linear=False), [1])

    def test_shortcuts(self):
        """Check if '/' and '//' work as '.search' and '.catalyse'."""
        self.assertEqual(EcoRI / self.ecosite_seq, [6])
        self.assertEqual(self.ecosite_seq / EcoRI, [6])
        self.assertEqual(len(EcoRI // self.ecosite_seq), 2)
        self.assertEqual(len(self.ecosite_seq // EcoRI), 2)

    def test_cutting_border_positions(self):
        """Check if cutting after first and penultimate position works."""
        # Use EarI, cuts as follows: CTCTTCN^NNN_N
        seq = Seq('CTCTTCA')
        self.assertEqual(EarI.search(seq), [])
        seq += 'A'
        self.assertEqual(EarI.search(seq), [8])
        # Recognition site on reverse-complement strand
        seq = Seq('AAAAGAAGAG')
        self.assertEqual(EarI.search(seq), [])
        seq = 'A' + seq
        self.assertEqual(EarI.search(seq), [2])

    def test_recognition_site_on_both_strands(self):
        """Check if recognition sites on both strands are properly handled."""
        seq = Seq('CTCTTCGAAGAG')
        self.assertEqual(EarI.search(seq), [3, 8])

    def test_overlapping_cut_sites(self):
        """Check if overlapping recognition sites are properly handled."""
        seq = Seq('CATGCACGCATGCATGCACGC')
        self.assertEqual(SphI.search(seq), [13, 17])


class EnzymeComparison(unittest.TestCase):
    """Tests for comparing various enzymes."""

    def test_basic_isochizomers(self):
        """Test to be sure isochizomer and neoschizomers are as expected."""
        self.assertEqual(Acc65I.isoschizomers(), [Asp718I, KpnI])
        self.assertEqual(Acc65I.elucidate(), 'G^GTAC_C')
        self.assertEqual(Asp718I.elucidate(), 'G^GTAC_C')
        self.assertEqual(KpnI.elucidate(), 'G_GTAC^C')
        self.assertTrue(Acc65I.is_isoschizomer(KpnI))
        self.assertFalse(Acc65I.is_equischizomer(KpnI))
        self.assertTrue(Acc65I.is_neoschizomer(KpnI))
        self.assertIn(Acc65I, Asp718I.equischizomers())
        self.assertIn(KpnI, Asp718I.neoschizomers())
        self.assertIn(KpnI, Acc65I.isoschizomers())

    def test_comparisons(self):
        """Test comparison operators between different enzymes."""
        # Comparison of iso- and neoschizomers
        self.assertEqual(Acc65I, Acc65I)
        self.assertNotEqual(Acc65I, KpnI)
        self.assertFalse(Acc65I == Asp718I)
        self.assertFalse(Acc65I != Asp718I)
        self.assertNotEqual(Acc65I, EcoRI)
        self.assertTrue(Acc65I >> KpnI)
        self.assertFalse(Acc65I >> Asp718I)

        # Compare length of recognition sites
        self.assertFalse(EcoRI >= EcoRV)
        self.assertTrue(EcoRV >= EcoRI)
        with self.assertRaises(NotImplementedError):
            EcoRV >= 3
        self.assertFalse(EcoRI > EcoRV)
        self.assertTrue(EcoRV > EcoRI)
        with self.assertRaises(NotImplementedError):
            EcoRV > 3
        self.assertTrue(EcoRI <= EcoRV)
        self.assertFalse(EcoRV <= EcoRI)
        with self.assertRaises(NotImplementedError):
            EcoRV <= 3
        self.assertTrue(EcoRI < EcoRV)
        self.assertFalse(EcoRV < EcoRI)
        with self.assertRaises(NotImplementedError):
            EcoRV < 3

        # Compare compatible overhangs
        self.assertTrue(Acc65I % Asp718I)
        self.assertTrue(Acc65I % Acc65I)
        self.assertFalse(Acc65I % KpnI)
        with self.assertRaises(TypeError):
            Acc65I % 'KpnI'
        self.assertTrue(SmaI % EcoRV)
        self.assertTrue(EarI % EarI)
        self.assertIn(EcoRV, SmaI.compatible_end())
        self.assertIn(Acc65I, Asp718I.compatible_end())


class RestrictionBatchPrintTest(unittest.TestCase):
    """Tests Restriction.Analysis printing functionality."""

    def createAnalysis(self, seq_str, batch_ary):
        """Restriction.Analysis creation helper method."""
        rb = Restriction.RestrictionBatch(batch_ary)
        seq = Seq(seq_str)
        return Restriction.Analysis(rb, seq)

    def assertAnalysisFormat(self, analysis, expected):
        """Test make_format.

        Test that the Restriction.Analysis make_format(print_that) matches
        some string.
        """
        dct = analysis.mapping
        ls, nc = [], []
        for k, v in dct.items():
            if v:
                ls.append((k, v))
            else:
                nc.append(k)
        result = analysis.make_format(ls, '', [], '')
        self.assertEqual(result.replace(' ', ''), expected.replace(' ', ''))

    def test_make_format_map1(self):
        """Test that print_as('map'); print_that() correctly wraps round.

        1. With no marker.
        """
        analysis = self.createAnalysis(
            'CCAGTCTATAATTCG' +
            Restriction.BamHI.site +
            'GCGGCATCATACTCGAATATCGCGTGATGATACGTAGTAATTACGCATG',
            ["BamHI"])
        analysis.print_as('map')
        expected = [
            "                17 BamHI",
            "                |                                           ",
            "CCAGTCTATAATTCGGGATCCGCGGCATCATACTCGAATATCGCGTGATGATACGTAGTA",
            "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||",
            "GGTCAGATATTAAGCCCTAGGCGCCGTAGTATGAGCTTATAGCGCACTACTATGCATCAT",
            "1                                                         60",
            "",
            "ATTACGCATG",
            "||||||||||",
            "TAATGCGTAC",
            "61                          70",
            "", ""]
        self.assertAnalysisFormat(analysis, '\n'.join(expected))

    def test_make_format_map2(self):
        """Test that print_as('map'); print_that() correctly wraps round.

        2. With marker.
        """
        analysis = self.createAnalysis(
            'CCAGTCTATAATTCG' +
            Restriction.BamHI.site +
            'GCGGCATCATACTCGA' +
            Restriction.BamHI.site +
            'ATATCGCGTGATGATA' +
            Restriction.NdeI.site +
            'CGTAGTAATTACGCATG',
            ["NdeI", "EcoRI", "BamHI", "BsmBI"])
        analysis.print_as('map')
        expected = [
            "                17 BamHI",
            "                |                                           ",
            "                |                     39 BamHI",
            "                |                     |                     ",
            "CCAGTCTATAATTCGGGATCCGCGGCATCATACTCGAGGATCCATATCGCGTGATGATAC",
            "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||",
            "GGTCAGATATTAAGCCCTAGGCGCCGTAGTATGAGCTCCTAGGTATAGCGCACTACTATG",
            "1                                                         60",
            "",
            " 62 NdeI",
            " |                                                          ",
            "ATATGCGTAGTAATTACGCATG",
            "||||||||||||||||||||||",
            "TATACGCATCATTAATGCGTAC",
            "61                          82",
            "", ""]
        self.assertAnalysisFormat(analysis, '\n'.join(expected))

    def test_make_format_map3(self):
        """Test that print_as('map'); print_that() correctly wraps round.

        3. With marker restricted.
        """
        analysis = self.createAnalysis(
            'CCAGTCTATAATTCG' +
            Restriction.BamHI.site +
            'GCGGCATCATACTCGA' +
            Restriction.BamHI.site +
            'ATATCGCGTGATGATA' +
            Restriction.EcoRV.site +
            'CGTAGTAATTACGCATG',
            ["NdeI", "EcoRI", "BamHI", "BsmBI"])
        analysis.print_as('map')
        expected = [
            "                17 BamHI",
            "                |                                           ",
            "                |                     39 BamHI",
            "                |                     |                     ",
            "CCAGTCTATAATTCGGGATCCGCGGCATCATACTCGAGGATCCATATCGCGTGATGATAG",
            "||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||",
            "GGTCAGATATTAAGCCCTAGGCGCCGTAGTATGAGCTCCTAGGTATAGCGCACTACTATC",
            "1                                                         60",
            "",
            "ATATCCGTAGTAATTACGCATG",
            "||||||||||||||||||||||",
            "TATAGGCATCATTAATGCGTAC",
            "61                          82",
            "", ""]
        self.assertAnalysisFormat(analysis, '\n'.join(expected))

    def test_change(self):
        """Test that change() changes something."""
        seq = Seq('CCAGTCTATAATTCG' + BamHI.site +
                  'GCGGCATCATACTCGA' + BamHI.site +
                  'ATATCGCGTGATGATA' + EcoRV.site +
                  'CGTAGTAATTACGCATG')
        batch = NdeI + EcoRI + BamHI + BsmBI
        analysis = Analysis(batch, seq)
        self.assertEqual(analysis.full()[BamHI], [17, 39])
        batch = NdeI + EcoRI + BsmBI
        seq += NdeI.site
        analysis.change(sequence=seq)
        analysis.change(rb=batch)
        self.assertEqual(len(analysis.full()), 3)
        self.assertEqual(analysis.full()[NdeI], [85])
        with self.assertRaises(AttributeError):
            analysis.change(**{'NameWidth': 3, 'KonsoleWidth': 40})  # Console


class RestrictionBatches(unittest.TestCase):
    """Tests for dealing with batches of restriction enzymes."""

    def test_creating_batch(self):
        """Creating and modifying a restriction batch."""
        batch = RestrictionBatch()
        self.assertEqual(batch.suppl_codes()['N'], 'New England Biolabs')
        self.assertTrue(batch.is_restriction(EcoRI))
        batch = RestrictionBatch([EcoRI])
        batch.add(KpnI)
        batch += EcoRV
        self.assertEqual(len(batch), 3)
        self.assertEqual(batch.elements(), ['EcoRI', 'EcoRV', 'KpnI'])
        # Problem with Python 3, as sequence of list may be different:
        # self.assertEqual(batch.as_string(), ['EcoRI', 'KpnI', 'EcoRV'])
        self.assertIn('EcoRI', batch.as_string())

        # The usual way to test batch membership
        self.assertIn(EcoRV, batch)
        self.assertIn(EcoRI, batch)
        self.assertIn(KpnI, batch)
        self.assertNotIn(SmaI, batch)
        # Syntax sugar for the above
        self.assertIn('EcoRV', batch)
        self.assertNotIn('SmaI', batch)

        batch.get(EcoRV)
        self.assertRaises(ValueError, batch.get, SmaI)
        batch.get(SmaI, add=True)
        self.assertEqual(len(batch), 4)
        batch.remove(SmaI)
        batch.remove(EcoRV)
        self.assertEqual(len(batch), 2)

        self.assertNotIn(EcoRV, batch)
        self.assertNotIn('EcoRV', batch)

        # Creating a batch by addition of restriction enzymes
        new_batch = EcoRI + KpnI
        self.assertEqual(batch, new_batch)
        # or by addition of a batch with an enzyme
        another_new_batch = new_batch + EcoRV
        new_batch += EcoRV
        self.assertEqual(another_new_batch, new_batch)
        self.assertRaises(TypeError, EcoRI.__add__, 1)

        # Create a batch with suppliers and other supplier related methods
        # These tests may be 'update sensitive' since company names and
        # products may change often...
        batch = RestrictionBatch((), ('S'))  # Sigma
        self.assertEqual(batch.current_suppliers(),
                         ['Sigma Chemical Corporation'])
        self.assertIn(EcoRI, batch)
        self.assertNotIn(AanI, batch)
        batch.add_supplier('B')  # Life Technologies
        self.assertIn(AanI, batch)

    def test_batch_analysis(self):
        """Sequence analysis with a restriction batch."""
        seq = Seq("AAAA" + EcoRV.site + "AAAA" + EcoRI.site + "AAAA",
                  IUPACAmbiguousDNA())
        batch = RestrictionBatch([EcoRV, EcoRI])

        hits = batch.search(seq)
        self.assertEqual(hits[EcoRV], [8])
        self.assertEqual(hits[EcoRI], [16])

    def test_premade_batches(self):
        """Test content of premade batches CommOnly, NoComm, AllEnzymes."""
        self.assertTrue(len(AllEnzymes) == len(CommOnly) + len(NonComm))
        self.assertTrue(len(AllEnzymes) > len(CommOnly) > len(NonComm))

    def test_search_premade_batches(self):
        """Test search with pre-made batches CommOnly, NoComm, AllEnzymes."""
        seq = Seq('ACCCGAATTCAAAACTGACTGATCGATCGTCGACTG', IUPACAmbiguousDNA())
        search = AllEnzymes.search(seq)
        self.assertEqual(search[MluCI], [6])
        # Check if '/' operator works as 'search':
        search = CommOnly / seq
        self.assertEqual(search[MluCI], [6])
        # Also in reverse order:
        search = seq / NonComm
        self.assertEqual(search[McrI], [28])

    def test_analysis_restrictions(self):
        """Test Fancier restriction analysis."""
        new_seq = Seq('TTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAA',
                      IUPACAmbiguousDNA())
        rb = RestrictionBatch([EcoRI, KpnI, EcoRV])
        ana = Analysis(rb, new_seq, linear=False)
        # Output only the result for enzymes which cut blunt:
        self.assertEqual(ana.blunt(), {EcoRV: []})
        self.assertEqual(ana.full(), {KpnI: [], EcoRV: [], EcoRI: [33]})
        # Output only the result for enzymes which have a site:
        self.assertEqual(ana.with_sites(), {EcoRI: [33]})
        # Output only the enzymes which have no site:
        self.assertEqual(ana.without_site(), {KpnI: [], EcoRV: []})
        self.assertEqual(ana.with_site_size([32]), {})
        # Output only enzymes which produce 5' overhangs
        self.assertEqual(ana.overhang5(), {EcoRI: [33]})
        # Output only enzymes which produce 3' overhangs
        self.assertEqual(ana.overhang3(), {KpnI: []})
        # Output only enzymes which produce defined ends
        self.assertEqual(ana.defined(), {KpnI: [], EcoRV: [], EcoRI: [33]})
        # Output only enzymes hich cut N times
        self.assertEqual(ana.with_N_sites(2), {})
        # The enzymes which cut between position x and y:
        with self.assertRaises(TypeError):
            ana.only_between('t', 20)
        with self.assertRaises(TypeError):
            ana.only_between(1, 't')
        self.assertEqual(ana.only_between(1, 20), {})
        self.assertEqual(ana.only_between(20, 34), {EcoRI: [33]})
        # Mix start/end order:
        self.assertEqual(ana.only_between(34, 20), {EcoRI: [33]})
        self.assertEqual(ana.only_outside(20, 34), {})
        with self.assertWarns(BiopythonWarning):
            ana.with_name(['fake'])
        self.assertEqual(ana.with_name([EcoRI]), {EcoRI: [33]})
        self.assertEqual((ana._boundaries(1, 20)[:2]), (1, 20))
        # Reverse order:
        self.assertEqual((ana._boundaries(20, 1)[:2]), (1, 20))
        # Fix negative start:
        self.assertEqual((ana._boundaries(-1, 20)[:2]), (20, 33))
        # Fix negative end:
        self.assertEqual((ana._boundaries(1, -1)[:2]), (1, 33))
        # Sites in- and outside of boundaries
        new_seq = Seq('GAATTCAAAAAAGAATTC', IUPACAmbiguousDNA())
        rb = RestrictionBatch([EcoRI])
        ana = Analysis(rb, new_seq)
        # Cut at least inside
        self.assertEqual(ana.between(1, 7), {EcoRI: [2, 14]})
        # Cut at least inside and report only inside site
        self.assertEqual(ana.show_only_between(1, 7), {EcoRI: [2]})
        # Cut at least outside
        self.assertEqual(ana.outside(1, 7), {EcoRI: [2, 14]})
        # Don't cut within
        self.assertEqual(ana.do_not_cut(7, 12), {EcoRI: [2, 14]})


class TestPrintOutputs(unittest.TestCase):
    """Class to test various print outputs."""

    import sys

    try:  # Python 2
        from StringIO import StringIO
    except ImportError:  # Python 3
        from io import StringIO

    def test_supplier(self):
        """Test output of supplier list for different enzyme types."""
        out = self.StringIO()
        self.sys.stdout = out
        EcoRI.suppliers()
        self.assertIn('Life Technologies', out.getvalue())
        self.assertEqual(SnaI.suppliers(), None)
        EcoRI.all_suppliers()  # Independent of enzyme, list of all suppliers
        self.assertIn('Agilent Technologies', out.getvalue())
        batch = EcoRI + SnaI
        batch.show_codes()
        self.assertIn('N = New England Biolabs', out.getvalue())
        self.sys.stdout = self.sys.__stdout__

    def test_print_that(self):
        """Test print_that function."""
        out = self.StringIO()
        self.sys.stdout = out
        my_batch = EcoRI + SmaI + KpnI
        my_seq = Seq('GAATTCCCGGGATATA')  # EcoRI and SmaI sites
        analysis = Analysis(my_batch, my_seq)
        analysis.print_that(None, title='My sequence\n\n',
                            s1='Non Cutters\n\n')
        self.assertIn('My sequence', out.getvalue())
        self.assertIn('Non Cutters', out.getvalue())
        self.assertIn('2.', out.getvalue())
        self.sys.stdout = self.sys.__stdout__

    def test_str_method(self):
        """Test __str__ and __repr__ outputs."""
        batch = EcoRI + SmaI + KpnI
        self.assertEqual(str(batch), 'EcoRI+KpnI+SmaI')
        batch += Asp718I
        batch += SnaI
        self.assertEqual(str(batch), 'Asp718I+EcoRI...SmaI+SnaI')
        self.assertEqual(repr(batch),
                         "RestrictionBatch(['Asp718I', 'EcoRI', 'KpnI', "
                         "'SmaI', 'SnaI'])")


if __name__ == "__main__":
    runner = unittest.TextTestRunner(verbosity=2)
    unittest.main(testRunner=runner)