diff --git a/Bio/motifs/__init__.py b/Bio/motifs/__init__.py index e434333fbcc..b17d9ba3388 100644 --- a/Bio/motifs/__init__.py +++ b/Bio/motifs/__init__.py @@ -31,7 +31,6 @@ from Bio import BiopythonDeprecationWarning from Bio.Align import Alignment -from Bio.Seq import reverse_complement, reverse_complement_rna def create(instances, alphabet="ACGT"): @@ -187,163 +186,14 @@ def read(handle, fmt, strict=True): return motif -class Instances(list): - """Class containing a list of sequences that made the motifs.""" - - def __init__(self, instances=None, alphabet="ACGT"): - """Initialize the class.""" - from Bio.Seq import MutableSeq - from Bio.Seq import Seq - - warnings.warn( - "The Instances class has been deprecated; please use the\n" - "Alignment class in Bio.Align instead.\n" - "To create a Motif instance, instead of" - "\n" - ">>> from Bio.motifs import Instances\n" - ">>> instances = Instances([Seq('ACGT'), Seq('ACCT'), Seq('AAGT')])\n" - ">>> motif = Motif(alphabet='ACGT', instances=instances)\n" - "\n" - "please use\n" - "\n" - ">>> from Bio.Align import Alignment\n" - ">>> alignment = Alignment([Seq('ACGT'), Seq('ACCT'), Seq('AAGT')])\n" - ">>> motif = Motif(alphabet='ACGT', alignment=alignment)\n", - BiopythonDeprecationWarning, - ) - if isinstance(instances, (Seq, MutableSeq, str)): - raise TypeError( - "instances should be iterator of Seq objects or strings. " - "If a single sequence is given, will treat each character " - "as a separate sequence." - ) - - length = None - if instances is not None: - sequences = [] - for instance in instances: - if length is None: - length = len(instance) - elif length != len(instance): - message = ( - "All instances should have the same length (%d found, %d expected)" - % (len(instance), length) - ) - raise ValueError(message) - if not isinstance(instance, Seq): - instance = Seq(str(instance)) - sequences.append(instance) - # no errors were raised; store the instances: - self.extend(sequences) - self.length = length - self.alphabet = alphabet - - def __str__(self): - """Return a string containing the sequences of the motif.""" - text = "" - for instance in self: - text += str(instance) + "\n" - return text - - def count(self): - """Count nucleotides in a position.""" - counts = {} - for letter in self.alphabet: - counts[letter] = [0] * self.length - for instance in self: - for position, letter in enumerate(instance): - counts[letter][position] += 1 - return counts - - def search(self, sequence): - """Find positions of motifs in a given sequence. - - This is a generator function, returning found positions of motif - instances in a given sequence. - """ - warnings.warn( - """instances.search(sequence) has been deprecated. Please use sequence.search(instances) instead, where sequence is a Seq object.""", - BiopythonDeprecationWarning, - ) - for pos in range(len(sequence) - self.length + 1): - for instance in self: - if instance == sequence[pos : pos + self.length]: - yield (pos, instance) - break # no other instance will fit (we don't want to return multiple hits) - - def reverse_complement(self): - """Compute reverse complement of sequences.""" - from Bio.Seq import MutableSeq - from Bio.Seq import Seq - from Bio.SeqRecord import SeqRecord - - instances = Instances(alphabet=self.alphabet) - instances.length = self.length - if sorted(self.alphabet) == ["A", "C", "G", "T"]: - for instance in self: - if isinstance(instance, (Seq, MutableSeq, SeqRecord)): - instance = instance.reverse_complement() - elif isinstance(instance, str): - instance = reverse_complement(instance) - else: - raise RuntimeError( - "instance has unexpected type %s" % type(instance) - ) - instances.append(instance) - elif sorted(self.alphabet) == ["A", "C", "G", "U"]: - for instance in self: - if isinstance(instance, (Seq, MutableSeq, SeqRecord)): - instance = instance.reverse_complement_rna() - elif isinstance(instance, str): - instance = reverse_complement_rna(instance) - else: - raise RuntimeError( - "instance has unexpected type %s" % type(instance) - ) - instances.append(instance) - else: - raise ValueError( - "Calculating reverse complement only works for DNA and RNA instances" - ) - return instances - - class Motif: """A class representing sequence motifs.""" - def __init__(self, alphabet="ACGT", alignment=None, counts=None, instances=None): + def __init__(self, alphabet="ACGT", alignment=None, counts=None): """Initialize the class.""" from . import matrix self.name = "" - if instances is not None and alignment is not None: - raise Exception( - ValueError, "Specify either alignment or instances, don't specify both" - ) - if isinstance(alignment, Instances): - instances = alignment - alignment = None - if instances is not None: - warnings.warn( - "The instances argument has been deprecated.\n" - "Instead of" - "\n" - ">>> instances = [Seq('ACGT'), Seq('ACCT'), Seq('AAGT')]\n" - ">>> motif = Motif(alphabet='ACGT', instances=instances)\n" - "\n" - "please use\n" - "\n" - ">>> from Bio.Align import Alignment\n" - ">>> alignment = Alignment([Seq('ACGT'), Seq('ACCT'), Seq('AAGT')])\n" - ">>> motif = Motif(alphabet='ACGT', alignment=alignment)\n", - BiopythonDeprecationWarning, - ) - if counts is not None: - raise Exception( - ValueError, "Specify either counts or instances, don't specify both" - ) - alignment = Alignment(instances) - alphabet = instances.alphabet if counts is not None and alignment is not None: raise Exception( ValueError, "Specify either counts or an alignment, don't specify both" @@ -494,17 +344,6 @@ def pssm(self): """Calculate and return the position specific scoring matrix for this motif.""" return self.pwm.log_odds(self._background) - @property - def instances(self): - """Return the sequences from which the motif was built.""" - warnings.warn( - """The instances attribute has been deprecated. Instead of mymotif.instances, please use mymotif.alignment.sequences.""", - BiopythonDeprecationWarning, - ) - if self.alignment is None: - return None - return self.alignment.sequences - def __str__(self, masked=False): """Return string representation of a motif.""" text = "" diff --git a/DEPRECATED.rst b/DEPRECATED.rst index a55faf188c6..977035037c1 100644 --- a/DEPRECATED.rst +++ b/DEPRECATED.rst @@ -203,15 +203,16 @@ The ``format`` method of the ``Motif`` class in ``Bio.motifs`` was deprecated in release 1.77, in favor of a ``__format__`` method that can be used from the ``format`` built-in function. This decision was reversed in release 1.79. The ``search`` method of the ``Instances`` class in ``Bio.motifs`` was -deprecated in release 1.82. Instead of ``instances.search(sequence)``, -``sequence.search(instances)`` can be used, where sequence is a Seq object. -This allows instances to have different lengths. +deprecated in release 1.82, and removed in release 1.86. Instead of +``instances.search(sequence)``, ``sequence.search(instances)`` can be used, +where sequence is a Seq object. This allows instances to have different lengths. The ``version`` parameter of the ``weblogo`` method of the ``Motif`` class in ``Bio.motifs`` was deprecated in release 1.83. Using the parameter has no effect. The ``Instances`` class and the ``instances`` argument of the ``Motif`` class -initializer in ``Bio.motifs`` were deprecated in release 1.82. Instead of +initializer in ``Bio.motifs`` were deprecated in release 1.82, and removed in +release 1.86. Instead of >>> from Bio.motifs import Instances >>> instances = Instances([Seq('ACGT'), Seq('ACCT'), Seq('AAGT')]) @@ -224,10 +225,10 @@ please use >>> motif = Motif(alphabet='ACGT', alignment=alignment) The ``instances`` attribute of the ``Motif`` class in ``Bio.motifs`` was -deprecated in release 1.82. Instead of ``mymotif.instances``, please use -``mymotif.alignment.sequences``. +deprecated in release 1.82, and removed in release 1.86. Instead of +``mymotif.instances``, please use ``mymotif.alignment.sequences``. -The ``Instance`` class in ``Bio.motifs.meme`` was deprecated in release 1.86. +The ``Instance`` class in ``Bio.motifs.meme`` was deprecated in release 1.85. This class is a subclass from ``Seq``, but does not provide any additional capabilities. Please use a ``Seq`` object instead. diff --git a/Tests/test_motifs.py b/Tests/test_motifs.py index a40856d1a95..983cd695531 100644 --- a/Tests/test_motifs.py +++ b/Tests/test_motifs.py @@ -21,7 +21,6 @@ "Install numpy if you want to use Bio.motifs." ) from None -from Bio import BiopythonDeprecationWarning from Bio import motifs from Bio.Seq import Seq @@ -266,20 +265,6 @@ def test_alignace_parsing(self): self.assertEqual(record.sequences[9], "SEQ10; M: CTCAATCGTAGA at 3") self.assertEqual(len(record), 16) self.assertEqual(record[0].alphabet, "ACGT") - # using the old instances property: - with self.assertWarns(BiopythonDeprecationWarning): - self.assertEqual(len(record[0].instances), 11) - self.assertEqual(record[0].instances[0], "TCTACGATTGAG") - self.assertEqual(record[0].instances[1], "TCTACGATTGAG") - self.assertEqual(record[0].instances[2], "TCTACGATTGAG") - self.assertEqual(record[0].instances[3], "TCTACGATTGAG") - self.assertEqual(record[0].instances[4], "TCTACGATTGAG") - self.assertEqual(record[0].instances[5], "TCTACGATTGAG") - self.assertEqual(record[0].instances[6], "TCTACGATTGAG") - self.assertEqual(record[0].instances[7], "TCTACGATTGAG") - self.assertEqual(record[0].instances[8], "TCTACGATTGAG") - self.assertEqual(record[0].instances[9], "TCAAAGATAGAG") - self.assertEqual(record[0].instances[10], "TCTACGATTGAG") self.assertEqual(len(record[0].alignment.sequences), 11) self.assertEqual(record[0].alignment.sequences[0], "TCTACGATTGAG") self.assertEqual(record[0].alignment.sequences[1], "TCTACGATTGAG") @@ -328,31 +313,6 @@ def test_alignace_parsing(self): ) self.assertEqual(motif.mask, (0, 1, 1, 1, 1, 1, 0, 1, 1)) self.assertEqual(record[1].alphabet, "ACGT") - # using the old instances property: - with self.assertWarns(BiopythonDeprecationWarning): - self.assertEqual(len(record[1].instances), 22) - self.assertEqual(record[1].instances[0], "GCGAAGGAAGCAGCGCGTGTG") - self.assertEqual(record[1].instances[1], "GGCACCGCCTCTACGATTGAG") - self.assertEqual(record[1].instances[2], "CAGAGCTTAGCATTGAACGCG") - self.assertEqual(record[1].instances[3], "CTAATGAAAGCAATGAGAGTG") - self.assertEqual(record[1].instances[4], "CTTGTGCCCTCTAAGCGTCCG") - self.assertEqual(record[1].instances[5], "GAGCACGACGCTTTGTACCTG") - self.assertEqual(record[1].instances[6], "CGGCACTTAGCAGCGTATCGT") - self.assertEqual(record[1].instances[7], "CTGGTTTCATCTACGATTGAG") - self.assertEqual(record[1].instances[8], "GGGCCAATAGCGGCGCCGGAG") - self.assertEqual(record[1].instances[9], "GTGGAGTTATCTTAGTGCGCG") - self.assertEqual(record[1].instances[10], "GAGAGGTTATCTACGATTGAG") - self.assertEqual(record[1].instances[11], "CTGCTCCCCGCATACAGCGCG") - self.assertEqual(record[1].instances[12], "CAGAACCGAGGTCCGGTACGG") - self.assertEqual(record[1].instances[13], "GTGCCCCAAGCTTACCCAGGG") - self.assertEqual(record[1].instances[14], "CGCCTCTGATCTACGATTGAG") - self.assertEqual(record[1].instances[15], "GTGCTCATAGGGACGTCGCGG") - self.assertEqual(record[1].instances[16], "CTGCCCCCCGCATAGTAGGGG") - self.assertEqual(record[1].instances[17], "GTAAAGAAATCGATGTGCCAG") - self.assertEqual(record[1].instances[18], "CACCTGCAATTGCTGGCAGCG") - self.assertEqual(record[1].instances[19], "GGCGGGCCATCCCTGTATGAA") - self.assertEqual(record[1].instances[20], "CTCCAGGTCGCATGGAGAGAG") - self.assertEqual(record[1].instances[21], "CCTCGGATCGCTTGGGAAGAG") self.assertEqual(len(record[1].alignment.sequences), 22) self.assertEqual(record[1].alignment.sequences[0], "GCGAAGGAAGCAGCGCGTGTG") self.assertEqual(record[1].alignment.sequences[1], "GGCACCGCCTCTACGATTGAG") @@ -437,27 +397,6 @@ def test_alignace_parsing(self): ) self.assertEqual(record[2].alphabet, "ACGT") - # using the old instances property: - with self.assertWarns(BiopythonDeprecationWarning): - self.assertEqual(len(record[2].instances), 18) - self.assertEqual(record[2].instances[0], "GTGCGCGAAGGAAGCAGCGCG") - self.assertEqual(record[2].instances[1], "CAGAGCTTAGCATTGAACGCG") - self.assertEqual(record[2].instances[2], "GTGCCCGATGACCACCCGTCG") - self.assertEqual(record[2].instances[3], "GCCCTCTAAGCGTCCGCGGAT") - self.assertEqual(record[2].instances[4], "GAGCACGACGCTTTGTACCTG") - self.assertEqual(record[2].instances[5], "CGGCACTTAGCAGCGTATCGT") - self.assertEqual(record[2].instances[6], "GGGCCAATAGCGGCGCCGGAG") - self.assertEqual(record[2].instances[7], "GCGCACTAAGATAACTCCACG") - self.assertEqual(record[2].instances[8], "CGGCCCGTTGTCCAGCAGACG") - self.assertEqual(record[2].instances[9], "CTGCTCCCCGCATACAGCGCG") - self.assertEqual(record[2].instances[10], "GTGCCCCAAGCTTACCCAGGG") - self.assertEqual(record[2].instances[11], "GTGCTCATAGGGACGTCGCGG") - self.assertEqual(record[2].instances[12], "CTGCCCCCCGCATAGTAGGGG") - self.assertEqual(record[2].instances[13], "CGCCGCCATGCGACGCAGAGG") - self.assertEqual(record[2].instances[14], "AACCTCTAAGCATACTCTACG") - self.assertEqual(record[2].instances[15], "GACCTGGAGGCTTAGACTTGG") - self.assertEqual(record[2].instances[16], "GCGCTCTTCCCAAGCGATCCG") - self.assertEqual(record[2].instances[17], "GGGCCGTCAGCTCTCAAGTCT") self.assertEqual(len(record[2].alignment.sequences), 18) self.assertEqual(record[2].alignment.sequences[0], "GTGCGCGAAGGAAGCAGCGCG") self.assertEqual(record[2].alignment.sequences[1], "CAGAGCTTAGCATTGAACGCG") @@ -530,25 +469,6 @@ def test_alignace_parsing(self): ) self.assertEqual(record[3].alphabet, "ACGT") - # using the old instances property: - with self.assertWarns(BiopythonDeprecationWarning): - self.assertEqual(len(record[3].instances), 16) - self.assertEqual(record[3].instances[0], "GCCCCAAGCTTACCCAGGGAC") - self.assertEqual(record[3].instances[1], "GCCGTCTGCTGGACAACGGGC") - self.assertEqual(record[3].instances[2], "GCCGACGGGTGGTCATCGGGC") - self.assertEqual(record[3].instances[3], "GCCAATAGCGGCGCCGGAGTC") - self.assertEqual(record[3].instances[4], "GCCCCCCGCATAGTAGGGGGA") - self.assertEqual(record[3].instances[5], "GCCCGTACCGGACCTCGGTTC") - self.assertEqual(record[3].instances[6], "GCCTCATGTACCGGAAGGGAC") - self.assertEqual(record[3].instances[7], "GACACGCGCCTGGGAGGGTTC") - self.assertEqual(record[3].instances[8], "GCCTTTGGCCTTGGATGAGAA") - self.assertEqual(record[3].instances[9], "GGCCCTCGGATCGCTTGGGAA") - self.assertEqual(record[3].instances[10], "GCATGTTGGGAATCCGCGGAC") - self.assertEqual(record[3].instances[11], "GACACGCGCTGTATGCGGGGA") - self.assertEqual(record[3].instances[12], "GCCAGGTACAAAGCGTCGTGC") - self.assertEqual(record[3].instances[13], "GCGATCAGCTTGTGGGCGTGC") - self.assertEqual(record[3].instances[14], "GACAAATCGGATACTGGGGCA") - self.assertEqual(record[3].instances[15], "GCACTTAGCAGCGTATCGTTA") self.assertEqual(len(record[3].alignment.sequences), 16) self.assertEqual(record[3].alignment.sequences[0], "GCCCCAAGCTTACCCAGGGAC") self.assertEqual(record[3].alignment.sequences[1], "GCCGTCTGCTGGACAACGGGC") @@ -614,24 +534,6 @@ def test_alignace_parsing(self): ACTTAGCAGCGTATCGTT""", ) self.assertEqual(record[4].alphabet, "ACGT") - # using the old instances property: - with self.assertWarns(BiopythonDeprecationWarning): - self.assertEqual(len(record[4].instances), 15) - self.assertEqual(record[4].instances[0], "CGGCACAGAGCTT") - self.assertEqual(record[4].instances[1], "ATCCGCGGACGCT") - self.assertEqual(record[4].instances[2], "CGCCTGGGAGGGT") - self.assertEqual(record[4].instances[3], "CGGAAGGGACGTT") - self.assertEqual(record[4].instances[4], "ACACACAGACGGT") - self.assertEqual(record[4].instances[5], "TGCCAGAGAGGTT") - self.assertEqual(record[4].instances[6], "AGACTGAGACGTT") - self.assertEqual(record[4].instances[7], "AATCGTAGAGGAT") - self.assertEqual(record[4].instances[8], "CGTCTCGTAGGGT") - self.assertEqual(record[4].instances[9], "CGTCGCGGAGGAT") - self.assertEqual(record[4].instances[10], "CTTCTTAGACGCT") - self.assertEqual(record[4].instances[11], "CGACGCAGAGGAT") - self.assertEqual(record[4].instances[12], "ATGCTTAGAGGTT") - self.assertEqual(record[4].instances[13], "AGACTTGGGCGAT") - self.assertEqual(record[4].instances[14], "CGACCTGGAGGCT") self.assertEqual(len(record[4].alignment.sequences), 15) self.assertEqual(record[4].alignment.sequences[0], "CGGCACAGAGCTT") self.assertEqual(record[4].alignment.sequences[1], "ATCCGCGGACGCT") @@ -691,27 +593,6 @@ def test_alignace_parsing(self): ACCTGGAGGC""", ) self.assertEqual(record[5].alphabet, "ACGT") - # using the old instances property: - with self.assertWarns(BiopythonDeprecationWarning): - self.assertEqual(len(record[5].instances), 18) - self.assertEqual(record[5].instances[0], "GTGCGCGAAGGAAGCAGCGCGTG") - self.assertEqual(record[5].instances[1], "TTGAGCCGAGTAAAGGGCTGGTG") - self.assertEqual(record[5].instances[2], "CAATGCTAAGCTCTGTGCCGACG") - self.assertEqual(record[5].instances[3], "CAACTCTCTATGTAGTGCCCGAG") - self.assertEqual(record[5].instances[4], "CGACGCTTTGTACCTGGCTTGCG") - self.assertEqual(record[5].instances[5], "CGAGTCAATGACACGCGCCTGGG") - self.assertEqual(record[5].instances[6], "CGATACGCTGCTAAGTGCCGTCC") - self.assertEqual(record[5].instances[7], "CCGGGCCAATAGCGGCGCCGGAG") - self.assertEqual(record[5].instances[8], "CCACGCTTCGACACGTGGTATAG") - self.assertEqual(record[5].instances[9], "CCGAGCCTCATGTACCGGAAGGG") - self.assertEqual(record[5].instances[10], "CTGCTCCCCGCATACAGCGCGTG") - self.assertEqual(record[5].instances[11], "CCGAGGTCCGGTACGGGCAAGCC") - self.assertEqual(record[5].instances[12], "GTGCTCATAGGGACGTCGCGGAG") - self.assertEqual(record[5].instances[13], "CCCTACTATGCGGGGGGCAGGTC") - self.assertEqual(record[5].instances[14], "GCCAGCAATTGCAGGTGGTCGTG") - self.assertEqual(record[5].instances[15], "CTCTGCGTCGCATGGCGGCGTGG") - self.assertEqual(record[5].instances[16], "GGAGGCTTAGACTTGGGCGATAC") - self.assertEqual(record[5].instances[17], "GCATGGAGAGAGATCCGGAGGAG") self.assertEqual(len(record[5].alignment.sequences), 18) self.assertEqual(record[5].alignment.sequences[0], "GTGCGCGAAGGAAGCAGCGCGTG") self.assertEqual(record[5].alignment.sequences[1], "TTGAGCCGAGTAAAGGGCTGGTG") @@ -783,29 +664,6 @@ def test_alignace_parsing(self): ATGGAGAGAGATCCGGAGGA""", ) self.assertEqual(record[6].alphabet, "ACGT") - # using the old instances property: - with self.assertWarns(BiopythonDeprecationWarning): - self.assertEqual(len(record[6].instances), 20) - self.assertEqual(record[6].instances[0], "GCGCGTGTGTGTAAC") - self.assertEqual(record[6].instances[1], "GCACAGAGCTTAGCA") - self.assertEqual(record[6].instances[2], "GGTGGTCATCGGGCA") - self.assertEqual(record[6].instances[3], "GCGCGTGTCATTGAC") - self.assertEqual(record[6].instances[4], "GGACGGCACTTAGCA") - self.assertEqual(record[6].instances[5], "GCGCGTCCCGGGCCA") - self.assertEqual(record[6].instances[6], "GCTCGGCCCGTTGTC") - self.assertEqual(record[6].instances[7], "GCGCGTGTCCTTTAA") - self.assertEqual(record[6].instances[8], "GCTGATCGCTGCTCC") - self.assertEqual(record[6].instances[9], "GCCCGTACCGGACCT") - self.assertEqual(record[6].instances[10], "GGACGTCGCGGAGGA") - self.assertEqual(record[6].instances[11], "GCGGGGGGCAGGTCA") - self.assertEqual(record[6].instances[12], "GGACGTACTGGCACA") - self.assertEqual(record[6].instances[13], "GCAGGTGGTCGTGCA") - self.assertEqual(record[6].instances[14], "GCGCATACCTTAACA") - self.assertEqual(record[6].instances[15], "GCACGGGACTTCAAC") - self.assertEqual(record[6].instances[16], "GCACGTAGCTGGTAA") - self.assertEqual(record[6].instances[17], "GCTCGTCTATGGTCA") - self.assertEqual(record[6].instances[18], "GCGCATGCTGGATCC") - self.assertEqual(record[6].instances[19], "GGCCGTCAGCTCTCA") self.assertEqual(len(record[6].alignment.sequences), 20) self.assertEqual(record[6].alignment.sequences[0], "GCGCGTGTGTGTAAC") self.assertEqual(record[6].alignment.sequences[1], "GCACAGAGCTTAGCA") @@ -880,29 +738,6 @@ def test_alignace_parsing(self): CCGTCAGCTCTC""", ) self.assertEqual(record[7].alphabet, "ACGT") - # using the old instances property: - with self.assertWarns(BiopythonDeprecationWarning): - self.assertEqual(len(record[7].instances), 20) - self.assertEqual(record[7].instances[0], "GAACCGAGGTCCGGTACGGGC") - self.assertEqual(record[7].instances[1], "GCCCCCCGCATAGTAGGGGGA") - self.assertEqual(record[7].instances[2], "GTCCCTGGGTAAGCTTGGGGC") - self.assertEqual(record[7].instances[3], "ACTCCACGCTTCGACACGTGG") - self.assertEqual(record[7].instances[4], "ATCCTCTGCGTCGCATGGCGG") - self.assertEqual(record[7].instances[5], "GTTCAATGCTAAGCTCTGTGC") - self.assertEqual(record[7].instances[6], "GCTCATAGGGACGTCGCGGAG") - self.assertEqual(record[7].instances[7], "GTCCCGGGCCAATAGCGGCGC") - self.assertEqual(record[7].instances[8], "GCACTTAGCAGCGTATCGTTA") - self.assertEqual(record[7].instances[9], "GGCCCTCGGATCGCTTGGGAA") - self.assertEqual(record[7].instances[10], "CTGCTGGACAACGGGCCGAGC") - self.assertEqual(record[7].instances[11], "GGGCACTACATAGAGAGTTGC") - self.assertEqual(record[7].instances[12], "AGCCTCCAGGTCGCATGGAGA") - self.assertEqual(record[7].instances[13], "AATCGTAGATCAGAGGCGAGA") - self.assertEqual(record[7].instances[14], "GAACTCCACTAAGACTTGAGA") - self.assertEqual(record[7].instances[15], "GAGCAGCGATCAGCTTGTGGG") - self.assertEqual(record[7].instances[16], "GCCAGGTACAAAGCGTCGTGC") - self.assertEqual(record[7].instances[17], "AGTCAATGACACGCGCCTGGG") - self.assertEqual(record[7].instances[18], "GGTCATGGAATCTTATGTAGC") - self.assertEqual(record[7].instances[19], "GTAGATAACAGAGGTCGGGGG") self.assertEqual(len(record[7].alignment.sequences), 20) self.assertEqual(record[7].alignment.sequences[0], "GAACCGAGGTCCGGTACGGGC") self.assertEqual(record[7].alignment.sequences[1], "GCCCCCCGCATAGTAGGGGGA") @@ -980,23 +815,6 @@ def test_alignace_parsing(self): AGATAACAGAGGTCGGGG""", ) self.assertEqual(record[8].alphabet, "ACGT") - # using the old instances property: - with self.assertWarns(BiopythonDeprecationWarning): - self.assertEqual(len(record[8].instances), 14) - self.assertEqual(record[8].instances[0], "CCGAGTAAAGGGCTG") - self.assertEqual(record[8].instances[1], "GTGGTCATCGGGCAC") - self.assertEqual(record[8].instances[2], "GATAACAGAGGTCGG") - self.assertEqual(record[8].instances[3], "CGGCGCCGGAGTCTG") - self.assertEqual(record[8].instances[4], "GCGCGTCCCGGGCCA") - self.assertEqual(record[8].instances[5], "CTGGACAACGGGCCG") - self.assertEqual(record[8].instances[6], "CGGATACTGGGGCAG") - self.assertEqual(record[8].instances[7], "GGGAGCAGCGATCAG") - self.assertEqual(record[8].instances[8], "CAGAACCGAGGTCCG") - self.assertEqual(record[8].instances[9], "GGGTCCCTGGGTAAG") - self.assertEqual(record[8].instances[10], "GTGCTCATAGGGACG") - self.assertEqual(record[8].instances[11], "GAGATCCGGAGGAGG") - self.assertEqual(record[8].instances[12], "GCGATCCGAGGGCCG") - self.assertEqual(record[8].instances[13], "GAGTTCACATGGCTG") self.assertEqual(len(record[8].alignment.sequences), 14) self.assertEqual(record[8].alignment.sequences[0], "CCGAGTAAAGGGCTG") self.assertEqual(record[8].alignment.sequences[1], "GTGGTCATCGGGCAC") @@ -1053,27 +871,6 @@ def test_alignace_parsing(self): GTTCACATGGCT""", ) self.assertEqual(record[9].alphabet, "ACGT") - # using the old instances property: - with self.assertWarns(BiopythonDeprecationWarning): - self.assertEqual(len(record[9].instances), 18) - self.assertEqual(record[9].instances[0], "TAGAGGCGGTG") - self.assertEqual(record[9].instances[1], "GCTAAGCTCTG") - self.assertEqual(record[9].instances[2], "TGGAAGCAGTG") - self.assertEqual(record[9].instances[3], "GCGAGGCTGTG") - self.assertEqual(record[9].instances[4], "ACGACGCTTTG") - self.assertEqual(record[9].instances[5], "GGGACGCGCAC") - self.assertEqual(record[9].instances[6], "TCGAAGCGTGG") - self.assertEqual(record[9].instances[7], "TGTATGCGGGG") - self.assertEqual(record[9].instances[8], "GGTAAGCTTGG") - self.assertEqual(record[9].instances[9], "TGTACGCTGGG") - self.assertEqual(record[9].instances[10], "ACTATGCGGGG") - self.assertEqual(record[9].instances[11], "GGTATGCGCTG") - self.assertEqual(record[9].instances[12], "GGTACCCGGAG") - self.assertEqual(record[9].instances[13], "GCGACGCAGAG") - self.assertEqual(record[9].instances[14], "TGGCGGCGTGG") - self.assertEqual(record[9].instances[15], "TCTAGGCGGGC") - self.assertEqual(record[9].instances[16], "AGTATGCTTAG") - self.assertEqual(record[9].instances[17], "TGGAGGCTTAG") self.assertEqual(len(record[9].alignment.sequences), 18) self.assertEqual(record[9].alignment.sequences[0], "TAGAGGCGGTG") self.assertEqual(record[9].alignment.sequences[1], "GCTAAGCTCTG") @@ -1142,22 +939,6 @@ def test_alignace_parsing(self): GAGGCTTA""", ) self.assertEqual(record[10].alphabet, "ACGT") - # using the old instances property: - with self.assertWarns(BiopythonDeprecationWarning): - self.assertEqual(len(record[10].instances), 13) - self.assertEqual(record[10].instances[0], "GCACAGAGCTTAGCATTGAAC") - self.assertEqual(record[10].instances[1], "GTCCGCGGATTCCCAACATGC") - self.assertEqual(record[10].instances[2], "ATACACAGCCTCGCAAGCCAG") - self.assertEqual(record[10].instances[3], "GGCCCGGGACGCGCACTAAGA") - self.assertEqual(record[10].instances[4], "GCCCGTTGTCCAGCAGACGGC") - self.assertEqual(record[10].instances[5], "GAGCAGCGATCAGCTTGTGGG") - self.assertEqual(record[10].instances[6], "GAACCGAGGTCCGGTACGGGC") - self.assertEqual(record[10].instances[7], "GTCCCTGGGTAAGCTTGGGGC") - self.assertEqual(record[10].instances[8], "GACCTGCCCCCCGCATAGTAG") - self.assertEqual(record[10].instances[9], "AACCAGCGCATACCTTAACAG") - self.assertEqual(record[10].instances[10], "ATCCTCTGCGTCGCATGGCGG") - self.assertEqual(record[10].instances[11], "GACCATAGACGAGCATCAAAG") - self.assertEqual(record[10].instances[12], "GGCCCTCGGATCGCTTGGGAA") self.assertEqual(len(record[10].alignment.sequences), 13) self.assertEqual(record[10].alignment.sequences[0], "GCACAGAGCTTAGCATTGAAC") self.assertEqual(record[10].alignment.sequences[1], "GTCCGCGGATTCCCAACATGC") @@ -1214,25 +995,6 @@ def test_alignace_parsing(self): CCCTCGGATCGCTTGGGA""", ) self.assertEqual(record[11].alphabet, "ACGT") - # using the old instances property: - with self.assertWarns(BiopythonDeprecationWarning): - self.assertEqual(len(record[11].instances), 16) - self.assertEqual(record[11].instances[0], "GCCGTCCGTC") - self.assertEqual(record[11].instances[1], "GGCGTGCGCG") - self.assertEqual(record[11].instances[2], "GGCGCGTGTC") - self.assertEqual(record[11].instances[3], "AGCGCGTGTG") - self.assertEqual(record[11].instances[4], "GCGGTGCGTG") - self.assertEqual(record[11].instances[5], "AGCGCGTGTC") - self.assertEqual(record[11].instances[6], "AGCGTCCGCG") - self.assertEqual(record[11].instances[7], "ACCGTCTGTG") - self.assertEqual(record[11].instances[8], "GCCATGCGAC") - self.assertEqual(record[11].instances[9], "ACCACCCGTC") - self.assertEqual(record[11].instances[10], "GGCGCCGGAG") - self.assertEqual(record[11].instances[11], "ACCACGTGTC") - self.assertEqual(record[11].instances[12], "GGCTTGCGAG") - self.assertEqual(record[11].instances[13], "GCGATCCGAG") - self.assertEqual(record[11].instances[14], "AGTGCGCGTC") - self.assertEqual(record[11].instances[15], "AGTGCCCGAG") self.assertEqual(len(record[11].alignment.sequences), 16) self.assertEqual(record[11].alignment.sequences[0], "GCCGTCCGTC") self.assertEqual(record[11].alignment.sequences[1], "GGCGTGCGCG") @@ -1295,25 +1057,6 @@ def test_alignace_parsing(self): TGCCCGA""", ) self.assertEqual(record[12].alphabet, "ACGT") - # using the old instances property: - with self.assertWarns(BiopythonDeprecationWarning): - self.assertEqual(len(record[12].instances), 16) - self.assertEqual(record[12].instances[0], "GCCGACGGGTGGTCATCGGG") - self.assertEqual(record[12].instances[1], "GCACGACGCTTTGTACCTGG") - self.assertEqual(record[12].instances[2], "CCTGGGAGGGTTCAATAACG") - self.assertEqual(record[12].instances[3], "GCGCGTCCCGGGCCAATAGC") - self.assertEqual(record[12].instances[4], "GCCGTCTGCTGGACAACGGG") - self.assertEqual(record[12].instances[5], "GTCCCTTCCGGTACATGAGG") - self.assertEqual(record[12].instances[6], "GCTGCTCCCCGCATACAGCG") - self.assertEqual(record[12].instances[7], "GCCCCAAGCTTACCCAGGGA") - self.assertEqual(record[12].instances[8], "ACCGGCTGACGCTAATACGG") - self.assertEqual(record[12].instances[9], "GCGGGGGGCAGGTCATTACA") - self.assertEqual(record[12].instances[10], "GCTGGCAGCGTCTAAGAAGG") - self.assertEqual(record[12].instances[11], "GCAGGTGGTCGTGCAATACG") - self.assertEqual(record[12].instances[12], "GCTGGTTGAAGTCCCGTGCG") - self.assertEqual(record[12].instances[13], "GCACGTAGCTGGTAAATAGG") - self.assertEqual(record[12].instances[14], "GCGGCGTGGATTTCATACAG") - self.assertEqual(record[12].instances[15], "CCTGGAGGCTTAGACTTGGG") self.assertEqual(len(record[12].alignment.sequences), 16) self.assertEqual(record[12].alignment.sequences[0], "GCCGACGGGTGGTCATCGGG") self.assertEqual(record[12].alignment.sequences[1], "GCACGACGCTTTGTACCTGG") @@ -1379,24 +1122,6 @@ def test_alignace_parsing(self): TGGAGGCTTAGACTTGG""", ) self.assertEqual(record[13].alphabet, "ACGT") - # using the old instances property: - with self.assertWarns(BiopythonDeprecationWarning): - self.assertEqual(len(record[13].instances), 15) - self.assertEqual(record[13].instances[0], "GCCGACGGGTGGTCATCGGG") - self.assertEqual(record[13].instances[1], "ATCCGCGGACGCTTAGAGGG") - self.assertEqual(record[13].instances[2], "ACGCTTTGTACCTGGCTTGC") - self.assertEqual(record[13].instances[3], "ACGGACGGCACTTAGCAGCG") - self.assertEqual(record[13].instances[4], "GCCGTCTGCTGGACAACGGG") - self.assertEqual(record[13].instances[5], "ACACACAGACGGTTGAAAGG") - self.assertEqual(record[13].instances[6], "GCCGATAGTGCTTAAGTTCG") - self.assertEqual(record[13].instances[7], "CTTGCCCGTACCGGACCTCG") - self.assertEqual(record[13].instances[8], "ACCGGCTGACGCTAATACGG") - self.assertEqual(record[13].instances[9], "GCCCCCCGCATAGTAGGGGG") - self.assertEqual(record[13].instances[10], "GCTGGCAGCGTCTAAGAAGG") - self.assertEqual(record[13].instances[11], "GCAGGTGGTCGTGCAATACG") - self.assertEqual(record[13].instances[12], "ACGCACGGGACTTCAACCAG") - self.assertEqual(record[13].instances[13], "GCACGTAGCTGGTAAATAGG") - self.assertEqual(record[13].instances[14], "ATCCTCTGCGTCGCATGGCG") self.assertEqual(len(record[13].alignment.sequences), 15) self.assertEqual(record[13].alignment.sequences[0], "GCCGACGGGTGGTCATCGGG") self.assertEqual(record[13].alignment.sequences[1], "ATCCGCGGACGCTTAGAGGG") @@ -1459,23 +1184,6 @@ def test_alignace_parsing(self): CCTCTGCGTCGCATGGC""", ) self.assertEqual(record[14].alphabet, "ACGT") - # using the old instances property: - with self.assertWarns(BiopythonDeprecationWarning): - self.assertEqual(len(record[14].instances), 14) - self.assertEqual(record[14].instances[0], "GAGGCTGTGTAT") - self.assertEqual(record[14].instances[1], "GAGGTCGGGGGT") - self.assertEqual(record[14].instances[2], "GACGGACGGCAC") - self.assertEqual(record[14].instances[3], "TTGGCCCGGGAC") - self.assertEqual(record[14].instances[4], "GAGGCTCGGCCC") - self.assertEqual(record[14].instances[5], "CACGCGCTGTAT") - self.assertEqual(record[14].instances[6], "TAGGCCAGGTAT") - self.assertEqual(record[14].instances[7], "GAGGTCCGGTAC") - self.assertEqual(record[14].instances[8], "TACGCTGGGGAT") - self.assertEqual(record[14].instances[9], "GTCGCGGAGGAT") - self.assertEqual(record[14].instances[10], "TACGCACGGGAC") - self.assertEqual(record[14].instances[11], "TACTCCGGGTAC") - self.assertEqual(record[14].instances[12], "GACGCAGAGGAT") - self.assertEqual(record[14].instances[13], "TAGGCGGGCCAT") self.assertEqual(len(record[14].alignment.sequences), 14) self.assertEqual(record[14].alignment.sequences[0], "GAGGCTGTGTAT") self.assertEqual(record[14].alignment.sequences[1], "GAGGTCGGGGGT") @@ -1532,30 +1240,6 @@ def test_alignace_parsing(self): GGCGGGCCA""", ) self.assertEqual(record[15].alphabet, "ACGT") - # using the old instances property: - with self.assertWarns(BiopythonDeprecationWarning): - self.assertEqual(len(record[15].instances), 21) - self.assertEqual(record[15].instances[0], "CGGCTCAATCGTAGAGGC") - self.assertEqual(record[15].instances[1], "CGACGGGTGGTCATCGGG") - self.assertEqual(record[15].instances[2], "CGCTTAGAGGGCACAAGC") - self.assertEqual(record[15].instances[3], "TGACACGCGCCTGGGAGG") - self.assertEqual(record[15].instances[4], "CGATACGCTGCTAAGTGC") - self.assertEqual(record[15].instances[5], "CGTCCCGGGCCAATAGCG") - self.assertEqual(record[15].instances[6], "CCACGCTTCGACACGTGG") - self.assertEqual(record[15].instances[7], "CGTCTGCTGGACAACGGG") - self.assertEqual(record[15].instances[8], "ACACAGACGGTTGAAAGG") - self.assertEqual(record[15].instances[9], "TGCTCCCCGCATACAGCG") - self.assertEqual(record[15].instances[10], "TGAGGCTTGCCCGTACCG") - self.assertEqual(record[15].instances[11], "TGCCCCAAGCTTACCCAG") - self.assertEqual(record[15].instances[12], "CGGCTGACGCTAATACGG") - self.assertEqual(record[15].instances[13], "CGCGACGTCCCTATGAGC") - self.assertEqual(record[15].instances[14], "TGCCCCCCGCATAGTAGG") - self.assertEqual(record[15].instances[15], "CGTTGCCTTCTTAGACGC") - self.assertEqual(record[15].instances[16], "TGACTCAATCGTAGACCC") - self.assertEqual(record[15].instances[17], "AGTCCCGTGCGTATGTGG") - self.assertEqual(record[15].instances[18], "AGGCTCGCACGTAGCTGG") - self.assertEqual(record[15].instances[19], "CCACGCCGCCATGCGACG") - self.assertEqual(record[15].instances[20], "AGCCTCCAGGTCGCATGG") self.assertEqual(len(record[15].alignment.sequences), 21) self.assertEqual(record[15].alignment.sequences[0], "CGGCTCAATCGTAGAGGC") self.assertEqual(record[15].alignment.sequences[1], "CGACGGGTGGTCATCGGG") @@ -3150,58 +2834,6 @@ def test_meme_parser_1(self): self.assertEqual(motif.num_occurrences, 7) self.assertAlmostEqual(motif.evalue, 0.19) self.assertEqual(motif.alphabet, "ACGT") - # using the old instances property: - with self.assertWarns(BiopythonDeprecationWarning): - self.assertEqual(len(motif.instances), 7) - self.assertAlmostEqual(motif.instances[0].pvalue, 1.21e-08, places=10) - self.assertAlmostEqual(motif.instances[1].pvalue, 1.87e-08, places=10) - self.assertAlmostEqual(motif.instances[2].pvalue, 6.62e-08, places=10) - self.assertAlmostEqual(motif.instances[3].pvalue, 1.05e-07, places=9) - self.assertAlmostEqual(motif.instances[4].pvalue, 1.69e-07, places=9) - self.assertAlmostEqual(motif.instances[5].pvalue, 5.62e-07, places=9) - self.assertAlmostEqual(motif.instances[6].pvalue, 1.08e-06, places=8) - self.assertEqual(motif.instances[0].sequence_name, "INO1") - self.assertEqual(motif.instances[1].sequence_name, "FAS1") - self.assertEqual(motif.instances[2].sequence_name, "ACC1") - self.assertEqual(motif.instances[3].sequence_name, "CHO2") - self.assertEqual(motif.instances[4].sequence_name, "CHO1") - self.assertEqual(motif.instances[5].sequence_name, "FAS2") - self.assertEqual(motif.instances[6].sequence_name, "OPI3") - self.assertEqual(motif.instances[0].sequence_id, "sequence_5") - self.assertEqual(motif.instances[1].sequence_id, "sequence_2") - self.assertEqual(motif.instances[2].sequence_id, "sequence_4") - self.assertEqual(motif.instances[3].sequence_id, "sequence_1") - self.assertEqual(motif.instances[4].sequence_id, "sequence_0") - self.assertEqual(motif.instances[5].sequence_id, "sequence_3") - self.assertEqual(motif.instances[6].sequence_id, "sequence_6") - self.assertEqual(motif.instances[0].strand, "+") - self.assertEqual(motif.instances[1].strand, "-") - self.assertEqual(motif.instances[2].strand, "-") - self.assertEqual(motif.instances[3].strand, "-") - self.assertEqual(motif.instances[4].strand, "-") - self.assertEqual(motif.instances[5].strand, "-") - self.assertEqual(motif.instances[6].strand, "+") - self.assertEqual(motif.instances[0].length, 13) - self.assertEqual(motif.instances[1].length, 13) - self.assertEqual(motif.instances[2].length, 13) - self.assertEqual(motif.instances[3].length, 13) - self.assertEqual(motif.instances[4].length, 13) - self.assertEqual(motif.instances[5].length, 13) - self.assertEqual(motif.instances[6].length, 13) - self.assertEqual(motif.instances[0].start, 620) - self.assertEqual(motif.instances[1].start, 94) - self.assertEqual(motif.instances[2].start, 82) - self.assertEqual(motif.instances[3].start, 353) - self.assertEqual(motif.instances[4].start, 639) - self.assertEqual(motif.instances[5].start, 566) - self.assertEqual(motif.instances[6].start, 585) - self.assertEqual(motif.instances[0], "GCGGCATGTGAAA") - self.assertEqual(motif.instances[1], "GCGGCATGTGAAG") - self.assertEqual(motif.instances[2], "GGGCCATGTGAAG") - self.assertEqual(motif.instances[3], "GCGGCATGAGAAA") - self.assertEqual(motif.instances[4], "GGTCCATGTGAAA") - self.assertEqual(motif.instances[5], "GTAGCATGTGAAA") - self.assertEqual(motif.instances[6], "AGTGCATGTGGAA") self.assertEqual(len(motif.alignment.sequences), 7) self.assertAlmostEqual(motif.alignment.sequences[0].pvalue, 1.21e-08, places=10) self.assertAlmostEqual(motif.alignment.sequences[1].pvalue, 1.87e-08, places=10) @@ -3283,51 +2915,6 @@ def test_meme_parser_1(self): self.assertEqual(motif.num_occurrences, 7) self.assertAlmostEqual(motif.evalue, 54) self.assertEqual(motif.alphabet, "ACGT") - # using the old instances property: - with self.assertWarns(BiopythonDeprecationWarning): - self.assertEqual(len(motif.instances), 7) - self.assertAlmostEqual(motif.instances[0].pvalue, 7.2e-10, places=11) - self.assertAlmostEqual(motif.instances[1].pvalue, 2.56e-08, places=10) - self.assertAlmostEqual(motif.instances[2].pvalue, 1.59e-07, places=9) - self.assertAlmostEqual(motif.instances[3].pvalue, 2.05e-07, places=9) - self.assertAlmostEqual(motif.instances[4].pvalue, 3.85e-07, places=9) - self.assertAlmostEqual(motif.instances[5].pvalue, 5.11e-07, places=9) - self.assertAlmostEqual(motif.instances[6].pvalue, 8.01e-07, places=9) - self.assertEqual(motif.instances[0].sequence_id, "sequence_1") - self.assertEqual(motif.instances[1].sequence_id, "sequence_6") - self.assertEqual(motif.instances[2].sequence_id, "sequence_4") - self.assertEqual(motif.instances[3].sequence_id, "sequence_0") - self.assertEqual(motif.instances[4].sequence_id, "sequence_2") - self.assertEqual(motif.instances[5].sequence_id, "sequence_3") - self.assertEqual(motif.instances[6].sequence_id, "sequence_5") - self.assertEqual(motif.instances[0].strand, "+") - self.assertEqual(motif.instances[1].strand, "-") - self.assertEqual(motif.instances[2].strand, "-") - self.assertEqual(motif.instances[3].strand, "+") - self.assertEqual(motif.instances[4].strand, "+") - self.assertEqual(motif.instances[5].strand, "-") - self.assertEqual(motif.instances[6].strand, "+") - self.assertEqual(motif.instances[0].length, 15) - self.assertEqual(motif.instances[1].length, 15) - self.assertEqual(motif.instances[2].length, 15) - self.assertEqual(motif.instances[3].length, 15) - self.assertEqual(motif.instances[4].length, 15) - self.assertEqual(motif.instances[5].length, 15) - self.assertEqual(motif.instances[6].length, 15) - self.assertEqual(motif.instances[0].start, 104) - self.assertEqual(motif.instances[1].start, 566) - self.assertEqual(motif.instances[2].start, 585) - self.assertEqual(motif.instances[3].start, 30) - self.assertEqual(motif.instances[4].start, 54) - self.assertEqual(motif.instances[5].start, 272) - self.assertEqual(motif.instances[6].start, 214) - self.assertEqual(motif.instances[0], "TTGACACCTGCCCAG") - self.assertEqual(motif.instances[1], "TTGACACCTACCCTG") - self.assertEqual(motif.instances[2], "TTGTCTCTTGCTCTG") - self.assertEqual(motif.instances[3], "TTGACACTTGATCAG") - self.assertEqual(motif.instances[4], "TTCACTACTCCCCTG") - self.assertEqual(motif.instances[5], "TTGACAACGGCTGGG") - self.assertEqual(motif.instances[6], "TTCACGCTTGCTACG") self.assertEqual(len(motif.alignment.sequences), 7) self.assertAlmostEqual(motif.alignment.sequences[0].pvalue, 7.2e-10, places=11) self.assertAlmostEqual(motif.alignment.sequences[1].pvalue, 2.56e-08, places=10) @@ -3453,240 +3040,6 @@ def test_meme_parser_2(self): self.assertEqual(motif.num_occurrences, 33) self.assertAlmostEqual(motif.evalue, 4.0e-129, places=130) self.assertEqual(motif.alphabet, "ACDEFGHIKLMNPQRSTVWY") - # using the old instances property: - with self.assertWarns(BiopythonDeprecationWarning): - self.assertEqual(len(motif.instances), 33) - self.assertAlmostEqual(motif.instances[0].pvalue, 8.78e-18, places=20) - self.assertAlmostEqual(motif.instances[1].pvalue, 1.41e-17, places=19) - self.assertAlmostEqual(motif.instances[2].pvalue, 1.42e-16, places=18) - self.assertAlmostEqual(motif.instances[3].pvalue, 2.75e-16, places=18) - self.assertAlmostEqual(motif.instances[4].pvalue, 3.55e-16, places=18) - self.assertAlmostEqual(motif.instances[5].pvalue, 3.55e-16, places=18) - self.assertAlmostEqual(motif.instances[6].pvalue, 1.74e-15, places=17) - self.assertAlmostEqual(motif.instances[7].pvalue, 3.87e-15, places=17) - self.assertAlmostEqual(motif.instances[8].pvalue, 4.84e-15, places=17) - self.assertAlmostEqual(motif.instances[9].pvalue, 1.04e-14, places=16) - self.assertAlmostEqual(motif.instances[10].pvalue, 1.58e-14, places=16) - self.assertAlmostEqual(motif.instances[11].pvalue, 1.76e-14, places=16) - self.assertAlmostEqual(motif.instances[12].pvalue, 2.16e-14, places=16) - self.assertAlmostEqual(motif.instances[13].pvalue, 2.94e-14, places=16) - self.assertAlmostEqual(motif.instances[14].pvalue, 3.25e-14, places=16) - self.assertAlmostEqual(motif.instances[15].pvalue, 3.98e-14, places=16) - self.assertAlmostEqual(motif.instances[16].pvalue, 4.39e-14, places=16) - self.assertAlmostEqual(motif.instances[17].pvalue, 4.39e-14, places=16) - self.assertAlmostEqual(motif.instances[18].pvalue, 4.85e-14, places=16) - self.assertAlmostEqual(motif.instances[19].pvalue, 6.52e-14, places=16) - self.assertAlmostEqual(motif.instances[20].pvalue, 1.41e-13, places=15) - self.assertAlmostEqual(motif.instances[21].pvalue, 1.55e-13, places=15) - self.assertAlmostEqual(motif.instances[22].pvalue, 3.07e-12, places=14) - self.assertAlmostEqual(motif.instances[23].pvalue, 5.43e-12, places=14) - self.assertAlmostEqual(motif.instances[24].pvalue, 6.91e-12, places=14) - self.assertAlmostEqual(motif.instances[25].pvalue, 8.76e-12, places=14) - self.assertAlmostEqual(motif.instances[26].pvalue, 9.48e-12, places=14) - self.assertAlmostEqual(motif.instances[27].pvalue, 1.2e-11, places=12) - self.assertAlmostEqual(motif.instances[28].pvalue, 1.19e-09, places=11) - self.assertAlmostEqual(motif.instances[29].pvalue, 1.54e-09, places=11) - self.assertAlmostEqual(motif.instances[30].pvalue, 1.99e-09, places=11) - self.assertAlmostEqual(motif.instances[31].pvalue, 1.42e-06, places=8) - self.assertAlmostEqual(motif.instances[32].pvalue, 3.43e-06, places=8) - self.assertEqual(motif.instances[0].sequence_name, "BUDC_KLETE") - self.assertEqual(motif.instances[1].sequence_name, "YINL_LISMO") - self.assertEqual(motif.instances[2].sequence_name, "DHII_HUMAN") - self.assertEqual(motif.instances[3].sequence_name, "HDE_CANTR") - self.assertEqual(motif.instances[4].sequence_name, "YRTP_BACSU") - self.assertEqual(motif.instances[5].sequence_name, "ENTA_ECOLI") - self.assertEqual(motif.instances[6].sequence_name, "HDHA_ECOLI") - self.assertEqual(motif.instances[7].sequence_name, "RIDH_KLEAE") - self.assertEqual(motif.instances[8].sequence_name, "DHB2_HUMAN") - self.assertEqual(motif.instances[9].sequence_name, "FIXR_BRAJA") - self.assertEqual(motif.instances[10].sequence_name, "PCR_PEA") - self.assertEqual(motif.instances[11].sequence_name, "DHCA_HUMAN") - self.assertEqual(motif.instances[12].sequence_name, "BDH_HUMAN") - self.assertEqual(motif.instances[13].sequence_name, "3BHD_COMTE") - self.assertEqual(motif.instances[14].sequence_name, "DHGB_BACME") - self.assertEqual(motif.instances[15].sequence_name, "DHMA_FLAS1") - self.assertEqual(motif.instances[16].sequence_name, "FVT1_HUMAN") - self.assertEqual(motif.instances[17].sequence_name, "BA72_EUBSP") - self.assertEqual(motif.instances[18].sequence_name, "BPHB_PSEPS") - self.assertEqual(motif.instances[19].sequence_name, "DHB3_HUMAN") - self.assertEqual(motif.instances[20].sequence_name, "DHES_HUMAN") - self.assertEqual(motif.instances[21].sequence_name, "AP27_MOUSE") - self.assertEqual(motif.instances[22].sequence_name, "2BHD_STREX") - self.assertEqual(motif.instances[23].sequence_name, "NODG_RHIME") - self.assertEqual(motif.instances[24].sequence_name, "HMTR_LEIMA") - self.assertEqual(motif.instances[25].sequence_name, "LIGD_PSEPA") - self.assertEqual(motif.instances[26].sequence_name, "MAS1_AGRRA") - self.assertEqual(motif.instances[27].sequence_name, "RFBB_NEIGO") - self.assertEqual(motif.instances[28].sequence_name, "GUTD_ECOLI") - self.assertEqual(motif.instances[29].sequence_name, "ADH_DROME") - self.assertEqual(motif.instances[30].sequence_name, "FABI_ECOLI") - self.assertEqual(motif.instances[31].sequence_name, "CSGA_MYXXA") - self.assertEqual(motif.instances[32].sequence_name, "YURA_MYXXA") - self.assertEqual(motif.instances[0].sequence_id, "sequence_7") - self.assertEqual(motif.instances[1].sequence_id, "sequence_20") - self.assertEqual(motif.instances[2].sequence_id, "sequence_10") - self.assertEqual(motif.instances[3].sequence_id, "sequence_15") - self.assertEqual(motif.instances[4].sequence_id, "sequence_21") - self.assertEqual(motif.instances[5].sequence_id, "sequence_12") - self.assertEqual(motif.instances[6].sequence_id, "sequence_16") - self.assertEqual(motif.instances[7].sequence_id, "sequence_19") - self.assertEqual(motif.instances[8].sequence_id, "sequence_23") - self.assertEqual(motif.instances[9].sequence_id, "sequence_13") - self.assertEqual(motif.instances[10].sequence_id, "sequence_30") - self.assertEqual(motif.instances[11].sequence_id, "sequence_25") - self.assertEqual(motif.instances[12].sequence_id, "sequence_5") - self.assertEqual(motif.instances[13].sequence_id, "sequence_1") - self.assertEqual(motif.instances[14].sequence_id, "sequence_9") - self.assertEqual(motif.instances[15].sequence_id, "sequence_11") - self.assertEqual(motif.instances[16].sequence_id, "sequence_27") - self.assertEqual(motif.instances[17].sequence_id, "sequence_4") - self.assertEqual(motif.instances[18].sequence_id, "sequence_6") - self.assertEqual(motif.instances[19].sequence_id, "sequence_24") - self.assertEqual(motif.instances[20].sequence_id, "sequence_8") - self.assertEqual(motif.instances[21].sequence_id, "sequence_3") - self.assertEqual(motif.instances[22].sequence_id, "sequence_0") - self.assertEqual(motif.instances[23].sequence_id, "sequence_18") - self.assertEqual(motif.instances[24].sequence_id, "sequence_28") - self.assertEqual(motif.instances[25].sequence_id, "sequence_17") - self.assertEqual(motif.instances[26].sequence_id, "sequence_29") - self.assertEqual(motif.instances[27].sequence_id, "sequence_31") - self.assertEqual(motif.instances[28].sequence_id, "sequence_14") - self.assertEqual(motif.instances[29].sequence_id, "sequence_2") - self.assertEqual(motif.instances[30].sequence_id, "sequence_26") - self.assertEqual(motif.instances[31].sequence_id, "sequence_22") - self.assertEqual(motif.instances[32].sequence_id, "sequence_32") - self.assertEqual(motif.instances[0].strand, "+") - self.assertEqual(motif.instances[1].strand, "+") - self.assertEqual(motif.instances[2].strand, "+") - self.assertEqual(motif.instances[3].strand, "+") - self.assertEqual(motif.instances[4].strand, "+") - self.assertEqual(motif.instances[5].strand, "+") - self.assertEqual(motif.instances[6].strand, "+") - self.assertEqual(motif.instances[7].strand, "+") - self.assertEqual(motif.instances[8].strand, "+") - self.assertEqual(motif.instances[9].strand, "+") - self.assertEqual(motif.instances[10].strand, "+") - self.assertEqual(motif.instances[11].strand, "+") - self.assertEqual(motif.instances[12].strand, "+") - self.assertEqual(motif.instances[13].strand, "+") - self.assertEqual(motif.instances[14].strand, "+") - self.assertEqual(motif.instances[15].strand, "+") - self.assertEqual(motif.instances[16].strand, "+") - self.assertEqual(motif.instances[17].strand, "+") - self.assertEqual(motif.instances[18].strand, "+") - self.assertEqual(motif.instances[19].strand, "+") - self.assertEqual(motif.instances[20].strand, "+") - self.assertEqual(motif.instances[21].strand, "+") - self.assertEqual(motif.instances[22].strand, "+") - self.assertEqual(motif.instances[23].strand, "+") - self.assertEqual(motif.instances[24].strand, "+") - self.assertEqual(motif.instances[25].strand, "+") - self.assertEqual(motif.instances[26].strand, "+") - self.assertEqual(motif.instances[27].strand, "+") - self.assertEqual(motif.instances[28].strand, "+") - self.assertEqual(motif.instances[29].strand, "+") - self.assertEqual(motif.instances[30].strand, "+") - self.assertEqual(motif.instances[31].strand, "+") - self.assertEqual(motif.instances[32].strand, "+") - self.assertEqual(motif.instances[0].length, 21) - self.assertEqual(motif.instances[1].length, 21) - self.assertEqual(motif.instances[2].length, 21) - self.assertEqual(motif.instances[3].length, 21) - self.assertEqual(motif.instances[4].length, 21) - self.assertEqual(motif.instances[5].length, 21) - self.assertEqual(motif.instances[6].length, 21) - self.assertEqual(motif.instances[7].length, 21) - self.assertEqual(motif.instances[8].length, 21) - self.assertEqual(motif.instances[9].length, 21) - self.assertEqual(motif.instances[10].length, 21) - self.assertEqual(motif.instances[11].length, 21) - self.assertEqual(motif.instances[12].length, 21) - self.assertEqual(motif.instances[13].length, 21) - self.assertEqual(motif.instances[14].length, 21) - self.assertEqual(motif.instances[15].length, 21) - self.assertEqual(motif.instances[16].length, 21) - self.assertEqual(motif.instances[17].length, 21) - self.assertEqual(motif.instances[18].length, 21) - self.assertEqual(motif.instances[19].length, 21) - self.assertEqual(motif.instances[20].length, 21) - self.assertEqual(motif.instances[21].length, 21) - self.assertEqual(motif.instances[22].length, 21) - self.assertEqual(motif.instances[23].length, 21) - self.assertEqual(motif.instances[24].length, 21) - self.assertEqual(motif.instances[25].length, 21) - self.assertEqual(motif.instances[26].length, 21) - self.assertEqual(motif.instances[27].length, 21) - self.assertEqual(motif.instances[28].length, 21) - self.assertEqual(motif.instances[29].length, 21) - self.assertEqual(motif.instances[30].length, 21) - self.assertEqual(motif.instances[31].length, 21) - self.assertEqual(motif.instances[32].length, 21) - self.assertEqual(motif.instances[0].start, 2) - self.assertEqual(motif.instances[1].start, 5) - self.assertEqual(motif.instances[2].start, 34) - self.assertEqual(motif.instances[3].start, 322) - self.assertEqual(motif.instances[4].start, 6) - self.assertEqual(motif.instances[5].start, 5) - self.assertEqual(motif.instances[6].start, 11) - self.assertEqual(motif.instances[7].start, 14) - self.assertEqual(motif.instances[8].start, 82) - self.assertEqual(motif.instances[9].start, 36) - self.assertEqual(motif.instances[10].start, 86) - self.assertEqual(motif.instances[11].start, 4) - self.assertEqual(motif.instances[12].start, 55) - self.assertEqual(motif.instances[13].start, 6) - self.assertEqual(motif.instances[14].start, 7) - self.assertEqual(motif.instances[15].start, 14) - self.assertEqual(motif.instances[16].start, 32) - self.assertEqual(motif.instances[17].start, 6) - self.assertEqual(motif.instances[18].start, 5) - self.assertEqual(motif.instances[19].start, 48) - self.assertEqual(motif.instances[20].start, 2) - self.assertEqual(motif.instances[21].start, 7) - self.assertEqual(motif.instances[22].start, 6) - self.assertEqual(motif.instances[23].start, 6) - self.assertEqual(motif.instances[24].start, 6) - self.assertEqual(motif.instances[25].start, 6) - self.assertEqual(motif.instances[26].start, 245) - self.assertEqual(motif.instances[27].start, 6) - self.assertEqual(motif.instances[28].start, 2) - self.assertEqual(motif.instances[29].start, 6) - self.assertEqual(motif.instances[30].start, 6) - self.assertEqual(motif.instances[31].start, 13) - self.assertEqual(motif.instances[32].start, 116) - self.assertEqual(motif.instances[0], "QKVALVTGAGQGIGKAIALRL") - self.assertEqual(motif.instances[1], "NKVIIITGASSGIGKATALLL") - self.assertEqual(motif.instances[2], "GKKVIVTGASKGIGREMAYHL") - self.assertEqual(motif.instances[3], "DKVVLITGAGAGLGKEYAKWF") - self.assertEqual(motif.instances[4], "HKTALITGGGRGIGRATALAL") - self.assertEqual(motif.instances[5], "GKNVWVTGAGKGIGYATALAF") - self.assertEqual(motif.instances[6], "GKCAIITGAGAGIGKEIAITF") - self.assertEqual(motif.instances[7], "GKVAAITGAASGIGLECARTL") - self.assertEqual(motif.instances[8], "QKAVLVTGGDCGLGHALCKYL") - self.assertEqual(motif.instances[9], "PKVMLLTGASRGIGHATAKLF") - self.assertEqual(motif.instances[10], "KGNVVITGASSGLGLATAKAL") - self.assertEqual(motif.instances[11], "IHVALVTGGNKGIGLAIVRDL") - self.assertEqual(motif.instances[12], "SKAVLVTGCDSGFGFSLAKHL") - self.assertEqual(motif.instances[13], "GKVALVTGGASGVGLEVVKLL") - self.assertEqual(motif.instances[14], "GKVVVITGSSTGLGKSMAIRF") - self.assertEqual(motif.instances[15], "GKAAIVTGAAGGIGRATVEAY") - self.assertEqual(motif.instances[16], "GAHVVVTGGSSGIGKCIAIEC") - self.assertEqual(motif.instances[17], "DKVTIITGGTRGIGFAAAKIF") - self.assertEqual(motif.instances[18], "GEAVLITGGASGLGRALVDRF") - self.assertEqual(motif.instances[19], "GQWAVITGAGDGIGKAYSFEL") - self.assertEqual(motif.instances[20], "RTVVLITGCSSGIGLHLAVRL") - self.assertEqual(motif.instances[21], "GLRALVTGAGKGIGRDTVKAL") - self.assertEqual(motif.instances[22], "GKTVIITGGARGLGAEAARQA") - self.assertEqual(motif.instances[23], "GRKALVTGASGAIGGAIARVL") - self.assertEqual(motif.instances[24], "VPVALVTGAAKRLGRSIAEGL") - self.assertEqual(motif.instances[25], "DQVAFITGGASGAGFGQAKVF") - self.assertEqual(motif.instances[26], "SPVILVSGSNRGVGKAIAEDL") - self.assertEqual(motif.instances[27], "KKNILVTGGAGFIGSAVVRHI") - self.assertEqual(motif.instances[28], "NQVAVVIGGGQTLGAFLCHGL") - self.assertEqual(motif.instances[29], "NKNVIFVAGLGGIGLDTSKEL") - self.assertEqual(motif.instances[30], "GKRILVTGVASKLSIAYGIAQ") - self.assertEqual(motif.instances[31], "VDVLINNAGVSGLWCALGDVD") - self.assertEqual(motif.instances[32], "IIDTNVTGAAATLSAVLPQMV") self.assertEqual(len(motif.alignment.sequences), 33) self.assertAlmostEqual(motif.alignment.sequences[0].pvalue, 8.78e-18, places=20) self.assertAlmostEqual(motif.alignment.sequences[1].pvalue, 1.41e-17, places=19) @@ -3968,174 +3321,6 @@ def test_meme_parser_2(self): self.assertEqual(motif.num_occurrences, 33) self.assertAlmostEqual(motif.evalue, 3.1e-130, places=131) self.assertEqual(motif.alphabet, "ACDEFGHIKLMNPQRSTVWY") - # using the old instances property: - with self.assertWarns(BiopythonDeprecationWarning): - self.assertEqual(len(motif.instances), 33) - self.assertAlmostEqual(motif.instances[0].pvalue, 2.09e-21, places=23) - self.assertAlmostEqual(motif.instances[1].pvalue, 7.63e-20, places=22) - self.assertAlmostEqual(motif.instances[2].pvalue, 6.49e-19, places=21) - self.assertAlmostEqual(motif.instances[3].pvalue, 1.92e-18, places=20) - self.assertAlmostEqual(motif.instances[4].pvalue, 5.46e-18, places=20) - self.assertAlmostEqual(motif.instances[5].pvalue, 6.21e-18, places=20) - self.assertAlmostEqual(motif.instances[6].pvalue, 4.52e-17, places=19) - self.assertAlmostEqual(motif.instances[7].pvalue, 4.52e-17, places=19) - self.assertAlmostEqual(motif.instances[8].pvalue, 9.21e-17, places=19) - self.assertAlmostEqual(motif.instances[9].pvalue, 1.65e-16, places=18) - self.assertAlmostEqual(motif.instances[10].pvalue, 2.07e-16, places=18) - self.assertAlmostEqual(motif.instances[11].pvalue, 3.65e-16, places=18) - self.assertAlmostEqual(motif.instances[12].pvalue, 5.7e-16, places=17) - self.assertAlmostEqual(motif.instances[13].pvalue, 5.7e-16, places=17) - self.assertAlmostEqual(motif.instances[14].pvalue, 7.93e-16, places=18) - self.assertAlmostEqual(motif.instances[15].pvalue, 8.85e-16, places=18) - self.assertAlmostEqual(motif.instances[16].pvalue, 1.1e-15, places=16) - self.assertAlmostEqual(motif.instances[17].pvalue, 1.69e-15, places=17) - self.assertAlmostEqual(motif.instances[18].pvalue, 3.54e-15, places=17) - self.assertAlmostEqual(motif.instances[19].pvalue, 4.83e-15, places=17) - self.assertAlmostEqual(motif.instances[20].pvalue, 7.27e-15, places=17) - self.assertAlmostEqual(motif.instances[21].pvalue, 9.85e-15, places=17) - self.assertAlmostEqual(motif.instances[22].pvalue, 2.41e-14, places=16) - self.assertAlmostEqual(motif.instances[23].pvalue, 2.66e-14, places=16) - self.assertAlmostEqual(motif.instances[24].pvalue, 1.22e-13, places=15) - self.assertAlmostEqual(motif.instances[25].pvalue, 5.18e-13, places=15) - self.assertAlmostEqual(motif.instances[26].pvalue, 1.24e-12, places=14) - self.assertAlmostEqual(motif.instances[27].pvalue, 1.35e-12, places=14) - self.assertAlmostEqual(motif.instances[28].pvalue, 5.59e-12, places=14) - self.assertAlmostEqual(motif.instances[29].pvalue, 1.44e-10, places=12) - self.assertAlmostEqual(motif.instances[30].pvalue, 1.61e-08, places=10) - self.assertAlmostEqual(motif.instances[31].pvalue, 4.26e-08, places=10) - self.assertAlmostEqual(motif.instances[32].pvalue, 1.16e-07, places=9) - self.assertEqual(motif.instances[0].sequence_name, "BUDC_KLETE") - self.assertEqual(motif.instances[1].sequence_name, "NODG_RHIME") - self.assertEqual(motif.instances[2].sequence_name, "FVT1_HUMAN") - self.assertEqual(motif.instances[3].sequence_name, "DHES_HUMAN") - self.assertEqual(motif.instances[4].sequence_name, "DHB3_HUMAN") - self.assertEqual(motif.instances[5].sequence_name, "YRTP_BACSU") - self.assertEqual(motif.instances[6].sequence_name, "HMTR_LEIMA") - self.assertEqual(motif.instances[7].sequence_name, "HDE_CANTR") - self.assertEqual(motif.instances[8].sequence_name, "DHGB_BACME") - self.assertEqual(motif.instances[9].sequence_name, "GUTD_ECOLI") - self.assertEqual(motif.instances[10].sequence_name, "3BHD_COMTE") - self.assertEqual(motif.instances[11].sequence_name, "DHII_HUMAN") - self.assertEqual(motif.instances[12].sequence_name, "BPHB_PSEPS") - self.assertEqual(motif.instances[13].sequence_name, "AP27_MOUSE") - self.assertEqual(motif.instances[14].sequence_name, "BDH_HUMAN") - self.assertEqual(motif.instances[15].sequence_name, "YINL_LISMO") - self.assertEqual(motif.instances[16].sequence_name, "FIXR_BRAJA") - self.assertEqual(motif.instances[17].sequence_name, "2BHD_STREX") - self.assertEqual(motif.instances[18].sequence_name, "RFBB_NEIGO") - self.assertEqual(motif.instances[19].sequence_name, "YURA_MYXXA") - self.assertEqual(motif.instances[20].sequence_name, "RIDH_KLEAE") - self.assertEqual(motif.instances[21].sequence_name, "DHMA_FLAS1") - self.assertEqual(motif.instances[22].sequence_name, "DHB2_HUMAN") - self.assertEqual(motif.instances[23].sequence_name, "HDHA_ECOLI") - self.assertEqual(motif.instances[24].sequence_name, "ENTA_ECOLI") - self.assertEqual(motif.instances[25].sequence_name, "LIGD_PSEPA") - self.assertEqual(motif.instances[26].sequence_name, "CSGA_MYXXA") - self.assertEqual(motif.instances[27].sequence_name, "BA72_EUBSP") - self.assertEqual(motif.instances[28].sequence_name, "ADH_DROME") - self.assertEqual(motif.instances[29].sequence_name, "MAS1_AGRRA") - self.assertEqual(motif.instances[30].sequence_name, "PCR_PEA") - self.assertEqual(motif.instances[31].sequence_name, "FABI_ECOLI") - self.assertEqual(motif.instances[32].sequence_name, "DHCA_HUMAN") - self.assertEqual(motif.instances[0].sequence_id, "sequence_7") - self.assertEqual(motif.instances[1].sequence_id, "sequence_18") - self.assertEqual(motif.instances[2].sequence_id, "sequence_27") - self.assertEqual(motif.instances[3].sequence_id, "sequence_8") - self.assertEqual(motif.instances[4].sequence_id, "sequence_24") - self.assertEqual(motif.instances[5].sequence_id, "sequence_21") - self.assertEqual(motif.instances[6].sequence_id, "sequence_28") - self.assertEqual(motif.instances[7].sequence_id, "sequence_15") - self.assertEqual(motif.instances[8].sequence_id, "sequence_9") - self.assertEqual(motif.instances[9].sequence_id, "sequence_14") - self.assertEqual(motif.instances[10].sequence_id, "sequence_1") - self.assertEqual(motif.instances[11].sequence_id, "sequence_10") - self.assertEqual(motif.instances[12].sequence_id, "sequence_6") - self.assertEqual(motif.instances[13].sequence_id, "sequence_3") - self.assertEqual(motif.instances[14].sequence_id, "sequence_5") - self.assertEqual(motif.instances[15].sequence_id, "sequence_20") - self.assertEqual(motif.instances[16].sequence_id, "sequence_13") - self.assertEqual(motif.instances[17].sequence_id, "sequence_0") - self.assertEqual(motif.instances[18].sequence_id, "sequence_31") - self.assertEqual(motif.instances[19].sequence_id, "sequence_32") - self.assertEqual(motif.instances[20].sequence_id, "sequence_19") - self.assertEqual(motif.instances[21].sequence_id, "sequence_11") - self.assertEqual(motif.instances[22].sequence_id, "sequence_23") - self.assertEqual(motif.instances[23].sequence_id, "sequence_16") - self.assertEqual(motif.instances[24].sequence_id, "sequence_12") - self.assertEqual(motif.instances[25].sequence_id, "sequence_17") - self.assertEqual(motif.instances[26].sequence_id, "sequence_22") - self.assertEqual(motif.instances[27].sequence_id, "sequence_4") - self.assertEqual(motif.instances[28].sequence_id, "sequence_2") - self.assertEqual(motif.instances[29].sequence_id, "sequence_29") - self.assertEqual(motif.instances[30].sequence_id, "sequence_30") - self.assertEqual(motif.instances[31].sequence_id, "sequence_26") - self.assertEqual(motif.instances[32].sequence_id, "sequence_25") - self.assertEqual(motif.instances[0].start, 144) - self.assertEqual(motif.instances[1].start, 144) - self.assertEqual(motif.instances[2].start, 178) - self.assertEqual(motif.instances[3].start, 147) - self.assertEqual(motif.instances[4].start, 190) - self.assertEqual(motif.instances[5].start, 147) - self.assertEqual(motif.instances[6].start, 185) - self.assertEqual(motif.instances[7].start, 459) - self.assertEqual(motif.instances[8].start, 152) - self.assertEqual(motif.instances[9].start, 146) - self.assertEqual(motif.instances[10].start, 143) - self.assertEqual(motif.instances[11].start, 175) - self.assertEqual(motif.instances[12].start, 145) - self.assertEqual(motif.instances[13].start, 141) - self.assertEqual(motif.instances[14].start, 200) - self.assertEqual(motif.instances[15].start, 146) - self.assertEqual(motif.instances[16].start, 181) - self.assertEqual(motif.instances[17].start, 144) - self.assertEqual(motif.instances[18].start, 157) - self.assertEqual(motif.instances[19].start, 152) - self.assertEqual(motif.instances[20].start, 152) - self.assertEqual(motif.instances[21].start, 157) - self.assertEqual(motif.instances[22].start, 224) - self.assertEqual(motif.instances[23].start, 151) - self.assertEqual(motif.instances[24].start, 136) - self.assertEqual(motif.instances[25].start, 149) - self.assertEqual(motif.instances[26].start, 80) - self.assertEqual(motif.instances[27].start, 149) - self.assertEqual(motif.instances[28].start, 144) - self.assertEqual(motif.instances[29].start, 384) - self.assertEqual(motif.instances[30].start, 18) - self.assertEqual(motif.instances[31].start, 177) - self.assertEqual(motif.instances[32].start, 144) - self.assertEqual(motif.instances[0], "VGNPELAVYSSSKFAVRGLTQTAARDLAP") - self.assertEqual(motif.instances[1], "IGNPGQTNYCASKAGMIGFSKSLAQEIAT") - self.assertEqual(motif.instances[2], "LGLFGFTAYSASKFAIRGLAEALQMEVKP") - self.assertEqual(motif.instances[3], "MGLPFNDVYCASKFALEGLCESLAVLLLP") - self.assertEqual(motif.instances[4], "FPWPLYSMYSASKAFVCAFSKALQEEYKA") - self.assertEqual(motif.instances[5], "RGAAVTSAYSASKFAVLGLTESLMQEVRK") - self.assertEqual(motif.instances[6], "QPLLGYTIYTMAKGALEGLTRSAALELAP") - self.assertEqual(motif.instances[7], "YGNFGQANYSSSKAGILGLSKTMAIEGAK") - self.assertEqual(motif.instances[8], "IPWPLFVHYAASKGGMKLMTETLALEYAP") - self.assertEqual(motif.instances[9], "VGSKHNSGYSAAKFGGVGLTQSLALDLAE") - self.assertEqual(motif.instances[10], "LPIEQYAGYSASKAAVSALTRAAALSCRK") - self.assertEqual(motif.instances[11], "VAYPMVAAYSASKFALDGFFSSIRKEYSV") - self.assertEqual(motif.instances[12], "YPNGGGPLYTAAKQAIVGLVRELAFELAP") - self.assertEqual(motif.instances[13], "VTFPNLITYSSTKGAMTMLTKAMAMELGP") - self.assertEqual(motif.instances[14], "MANPARSPYCITKFGVEAFSDCLRYEMYP") - self.assertEqual(motif.instances[15], "KAYPGGAVYGATKWAVRDLMEVLRMESAQ") - self.assertEqual(motif.instances[16], "VHPFAGSAYATSKAALASLTRELAHDYAP") - self.assertEqual(motif.instances[17], "MGLALTSSYGASKWGVRGLSKLAAVELGT") - self.assertEqual(motif.instances[18], "TPYAPSSPYSASKAAADHLVRAWQRTYRL") - self.assertEqual(motif.instances[19], "FRGLPATRYSASKAFLSTFMESLRVDLRG") - self.assertEqual(motif.instances[20], "VPVIWEPVYTASKFAVQAFVHTTRRQVAQ") - self.assertEqual(motif.instances[21], "MAEPEAAAYVAAKGGVAMLTRAMAVDLAR") - self.assertEqual(motif.instances[22], "APMERLASYGSSKAAVTMFSSVMRLELSK") - self.assertEqual(motif.instances[23], "NKNINMTSYASSKAAASHLVRNMAFDLGE") - self.assertEqual(motif.instances[24], "TPRIGMSAYGASKAALKSLALSVGLELAG") - self.assertEqual(motif.instances[25], "MGSALAGPYSAAKAASINLMEGYRQGLEK") - self.assertEqual(motif.instances[26], "NTDGGAYAYRMSKAALNMAVRSMSTDLRP") - self.assertEqual(motif.instances[27], "FGSLSGVGYPASKASVIGLTHGLGREIIR") - self.assertEqual(motif.instances[28], "NAIYQVPVYSGTKAAVVNFTSSLAKLAPI") - self.assertEqual(motif.instances[29], "RVLNPLVGYNMTKHALGGLTKTTQHVGWD") - self.assertEqual(motif.instances[30], "EGKIGASLKDSTLFGVSSLSDSLKGDFTS") - self.assertEqual(motif.instances[31], "MGPEGVRVNAISAGPIRTLAASGIKDFRK") - self.assertEqual(motif.instances[32], "RALKSCSPELQQKFRSETITEEELVGLMN") self.assertEqual(len(motif.alignment.sequences), 33) self.assertAlmostEqual(motif.alignment.sequences[0].pvalue, 2.09e-21, places=23) self.assertAlmostEqual(motif.alignment.sequences[1].pvalue, 7.63e-20, places=22) @@ -4367,177 +3552,6 @@ def test_meme_parser_3(self): self.assertEqual(motif.num_occurrences, 24) self.assertAlmostEqual(motif.evalue, 2.2e-94, places=95) self.assertEqual(motif.alphabet, "ACDEFGHIKLMNPQRSTVWY") - # using the old instances property: - with self.assertWarns(BiopythonDeprecationWarning): - self.assertEqual(len(motif.instances), 24) - self.assertAlmostEqual(motif.instances[0].pvalue, 6.98e-22, places=24) - self.assertAlmostEqual(motif.instances[1].pvalue, 4.67e-21, places=23) - self.assertAlmostEqual(motif.instances[2].pvalue, 1.25e-19, places=21) - self.assertAlmostEqual(motif.instances[3].pvalue, 1.56e-19, places=21) - self.assertAlmostEqual(motif.instances[4].pvalue, 2.44e-19, places=21) - self.assertAlmostEqual(motif.instances[5].pvalue, 6.47e-19, places=21) - self.assertAlmostEqual(motif.instances[6].pvalue, 8.9e-19, places=20) - self.assertAlmostEqual(motif.instances[7].pvalue, 2.53e-18, places=20) - self.assertAlmostEqual(motif.instances[8].pvalue, 1.27e-17, places=19) - self.assertAlmostEqual(motif.instances[9].pvalue, 2.77e-17, places=19) - self.assertAlmostEqual(motif.instances[10].pvalue, 4.93e-17, places=19) - self.assertAlmostEqual(motif.instances[11].pvalue, 7.19e-17, places=19) - self.assertAlmostEqual(motif.instances[12].pvalue, 8.68e-17, places=19) - self.assertAlmostEqual(motif.instances[13].pvalue, 2.62e-16, places=18) - self.assertAlmostEqual(motif.instances[14].pvalue, 2.87e-16, places=18) - self.assertAlmostEqual(motif.instances[15].pvalue, 7.66e-15, places=17) - self.assertAlmostEqual(motif.instances[16].pvalue, 2.21e-14, places=16) - self.assertAlmostEqual(motif.instances[17].pvalue, 3.29e-14, places=16) - self.assertAlmostEqual(motif.instances[18].pvalue, 7.21e-14, places=16) - self.assertAlmostEqual(motif.instances[19].pvalue, 1.14e-13, places=15) - self.assertAlmostEqual(motif.instances[20].pvalue, 1.67e-13, places=15) - self.assertAlmostEqual(motif.instances[21].pvalue, 4.42e-13, places=15) - self.assertAlmostEqual(motif.instances[22].pvalue, 5.11e-13, places=15) - self.assertAlmostEqual(motif.instances[23].pvalue, 2.82e-10, places=12) - self.assertEqual(motif.instances[0].sequence_name, "BET2_YEAST") - self.assertEqual(motif.instances[1].sequence_name, "RATRABGERB") - self.assertEqual(motif.instances[2].sequence_name, "CAL1_YEAST") - self.assertEqual(motif.instances[3].sequence_name, "PFTB_RAT") - self.assertEqual(motif.instances[4].sequence_name, "PFTB_RAT") - self.assertEqual(motif.instances[5].sequence_name, "RATRABGERB") - self.assertEqual(motif.instances[6].sequence_name, "RATRABGERB") - self.assertEqual(motif.instances[7].sequence_name, "BET2_YEAST") - self.assertEqual(motif.instances[8].sequence_name, "RATRABGERB") - self.assertEqual(motif.instances[9].sequence_name, "BET2_YEAST") - self.assertEqual(motif.instances[10].sequence_name, "RAM1_YEAST") - self.assertEqual(motif.instances[11].sequence_name, "BET2_YEAST") - self.assertEqual(motif.instances[12].sequence_name, "RAM1_YEAST") - self.assertEqual(motif.instances[13].sequence_name, "PFTB_RAT") - self.assertEqual(motif.instances[14].sequence_name, "RAM1_YEAST") - self.assertEqual(motif.instances[15].sequence_name, "PFTB_RAT") - self.assertEqual(motif.instances[16].sequence_name, "RATRABGERB") - self.assertEqual(motif.instances[17].sequence_name, "PFTB_RAT") - self.assertEqual(motif.instances[18].sequence_name, "BET2_YEAST") - self.assertEqual(motif.instances[19].sequence_name, "CAL1_YEAST") - self.assertEqual(motif.instances[20].sequence_name, "RAM1_YEAST") - self.assertEqual(motif.instances[21].sequence_name, "CAL1_YEAST") - self.assertEqual(motif.instances[22].sequence_name, "RAM1_YEAST") - self.assertEqual(motif.instances[23].sequence_name, "BET2_YEAST") - self.assertEqual(motif.instances[0].sequence_id, "sequence_2") - self.assertEqual(motif.instances[1].sequence_id, "sequence_3") - self.assertEqual(motif.instances[2].sequence_id, "sequence_4") - self.assertEqual(motif.instances[3].sequence_id, "sequence_1") - self.assertEqual(motif.instances[4].sequence_id, "sequence_1") - self.assertEqual(motif.instances[5].sequence_id, "sequence_3") - self.assertEqual(motif.instances[6].sequence_id, "sequence_3") - self.assertEqual(motif.instances[7].sequence_id, "sequence_2") - self.assertEqual(motif.instances[8].sequence_id, "sequence_3") - self.assertEqual(motif.instances[9].sequence_id, "sequence_2") - self.assertEqual(motif.instances[10].sequence_id, "sequence_0") - self.assertEqual(motif.instances[11].sequence_id, "sequence_2") - self.assertEqual(motif.instances[12].sequence_id, "sequence_0") - self.assertEqual(motif.instances[13].sequence_id, "sequence_1") - self.assertEqual(motif.instances[14].sequence_id, "sequence_0") - self.assertEqual(motif.instances[15].sequence_id, "sequence_1") - self.assertEqual(motif.instances[16].sequence_id, "sequence_3") - self.assertEqual(motif.instances[17].sequence_id, "sequence_1") - self.assertEqual(motif.instances[18].sequence_id, "sequence_2") - self.assertEqual(motif.instances[19].sequence_id, "sequence_4") - self.assertEqual(motif.instances[20].sequence_id, "sequence_0") - self.assertEqual(motif.instances[21].sequence_id, "sequence_4") - self.assertEqual(motif.instances[22].sequence_id, "sequence_0") - self.assertEqual(motif.instances[23].sequence_id, "sequence_2") - self.assertEqual(motif.instances[0].strand, "+") - self.assertEqual(motif.instances[1].strand, "+") - self.assertEqual(motif.instances[2].strand, "+") - self.assertEqual(motif.instances[3].strand, "+") - self.assertEqual(motif.instances[4].strand, "+") - self.assertEqual(motif.instances[5].strand, "+") - self.assertEqual(motif.instances[6].strand, "+") - self.assertEqual(motif.instances[7].strand, "+") - self.assertEqual(motif.instances[8].strand, "+") - self.assertEqual(motif.instances[9].strand, "+") - self.assertEqual(motif.instances[10].strand, "+") - self.assertEqual(motif.instances[11].strand, "+") - self.assertEqual(motif.instances[12].strand, "+") - self.assertEqual(motif.instances[13].strand, "+") - self.assertEqual(motif.instances[14].strand, "+") - self.assertEqual(motif.instances[15].strand, "+") - self.assertEqual(motif.instances[16].strand, "+") - self.assertEqual(motif.instances[17].strand, "+") - self.assertEqual(motif.instances[18].strand, "+") - self.assertEqual(motif.instances[19].strand, "+") - self.assertEqual(motif.instances[20].strand, "+") - self.assertEqual(motif.instances[21].strand, "+") - self.assertEqual(motif.instances[22].strand, "+") - self.assertEqual(motif.instances[23].strand, "+") - self.assertEqual(motif.instances[0].length, 30) - self.assertEqual(motif.instances[1].length, 30) - self.assertEqual(motif.instances[2].length, 30) - self.assertEqual(motif.instances[3].length, 30) - self.assertEqual(motif.instances[4].length, 30) - self.assertEqual(motif.instances[5].length, 30) - self.assertEqual(motif.instances[6].length, 30) - self.assertEqual(motif.instances[7].length, 30) - self.assertEqual(motif.instances[8].length, 30) - self.assertEqual(motif.instances[9].length, 30) - self.assertEqual(motif.instances[10].length, 30) - self.assertEqual(motif.instances[11].length, 30) - self.assertEqual(motif.instances[12].length, 30) - self.assertEqual(motif.instances[13].length, 30) - self.assertEqual(motif.instances[14].length, 30) - self.assertEqual(motif.instances[15].length, 30) - self.assertEqual(motif.instances[16].length, 30) - self.assertEqual(motif.instances[17].length, 30) - self.assertEqual(motif.instances[18].length, 30) - self.assertEqual(motif.instances[19].length, 30) - self.assertEqual(motif.instances[20].length, 30) - self.assertEqual(motif.instances[21].length, 30) - self.assertEqual(motif.instances[22].length, 30) - self.assertEqual(motif.instances[23].length, 30) - self.assertEqual(motif.instances[0].start, 223) - self.assertEqual(motif.instances[1].start, 227) - self.assertEqual(motif.instances[2].start, 275) - self.assertEqual(motif.instances[3].start, 237) - self.assertEqual(motif.instances[4].start, 138) - self.assertEqual(motif.instances[5].start, 179) - self.assertEqual(motif.instances[6].start, 131) - self.assertEqual(motif.instances[7].start, 172) - self.assertEqual(motif.instances[8].start, 276) - self.assertEqual(motif.instances[9].start, 124) - self.assertEqual(motif.instances[10].start, 247) - self.assertEqual(motif.instances[11].start, 272) - self.assertEqual(motif.instances[12].start, 145) - self.assertEqual(motif.instances[13].start, 286) - self.assertEqual(motif.instances[14].start, 296) - self.assertEqual(motif.instances[15].start, 348) - self.assertEqual(motif.instances[16].start, 83) - self.assertEqual(motif.instances[17].start, 189) - self.assertEqual(motif.instances[18].start, 73) - self.assertEqual(motif.instances[19].start, 205) - self.assertEqual(motif.instances[20].start, 198) - self.assertEqual(motif.instances[21].start, 327) - self.assertEqual(motif.instances[22].start, 349) - self.assertEqual(motif.instances[23].start, 24) - self.assertEqual(motif.instances[0], "GGLNGRPSKLPDVCYSWWVLSSLAIIGRLD") - self.assertEqual(motif.instances[1], "GGLNGRPEKLPDVCYSWWVLASLKIIGRLH") - self.assertEqual(motif.instances[2], "GGFQGRENKFADTCYAFWCLNSLHLLTKDW") - self.assertEqual(motif.instances[3], "GGIGGVPGMEAHGGYTFCGLAALVILKKER") - self.assertEqual(motif.instances[4], "GGFGGGPGQYPHLAPTYAAVNALCIIGTEE") - self.assertEqual(motif.instances[5], "GGFGCRPGSESHAGQIYCCTGFLAITSQLH") - self.assertEqual(motif.instances[6], "GSFAGDIWGEIDTRFSFCAVATLALLGKLD") - self.assertEqual(motif.instances[7], "GGFGLCPNAESHAAQAFTCLGALAIANKLD") - self.assertEqual(motif.instances[8], "GGFADRPGDMVDPFHTLFGIAGLSLLGEEQ") - self.assertEqual(motif.instances[9], "GSFQGDRFGEVDTRFVYTALSALSILGELT") - self.assertEqual(motif.instances[10], "GFGSCPHVDEAHGGYTFCATASLAILRSMD") - self.assertEqual(motif.instances[11], "GGISDRPENEVDVFHTVFGVAGLSLMGYDN") - self.assertEqual(motif.instances[12], "GPFGGGPGQLSHLASTYAAINALSLCDNID") - self.assertEqual(motif.instances[13], "GGFQGRCNKLVDGCYSFWQAGLLPLLHRAL") - self.assertEqual(motif.instances[14], "RGFCGRSNKLVDGCYSFWVGGSAAILEAFG") - self.assertEqual(motif.instances[15], "GGLLDKPGKSRDFYHTCYCLSGLSIAQHFG") - self.assertEqual(motif.instances[16], "GGVSASIGHDPHLLYTLSAVQILTLYDSIH") - self.assertEqual(motif.instances[17], "GSFLMHVGGEVDVRSAYCAASVASLTNIIT") - self.assertEqual(motif.instances[18], "GAFAPFPRHDAHLLTTLSAVQILATYDALD") - self.assertEqual(motif.instances[19], "YNGAFGAHNEPHSGYTSCALSTLALLSSLE") - self.assertEqual(motif.instances[20], "GFKTCLEVGEVDTRGIYCALSIATLLNILT") - self.assertEqual(motif.instances[21], "GGFSKNDEEDADLYHSCLGSAALALIEGKF") - self.assertEqual(motif.instances[22], "PGLRDKPGAHSDFYHTNYCLLGLAVAESSY") - self.assertEqual(motif.instances[23], "HNFEYWLTEHLRLNGIYWGLTALCVLDSPE") self.assertEqual(len(motif.alignment.sequences), 24) self.assertAlmostEqual(motif.alignment.sequences[0].pvalue, 6.98e-22, places=24) self.assertAlmostEqual(motif.alignment.sequences[1].pvalue, 4.67e-21, places=23) @@ -4931,156 +3945,6 @@ def test_meme_parser_3(self): self.assertEqual(motif.alignment.sequences[18], "LQREKHFHYLKRGL") self.assertEqual(motif.alignment.sequences[19], "DRKVRLISFIRGNQ") self.assertEqual(motif.alignment.sequences[20], "VNRMAIIFYSISGL") - # using the old instances property: - with self.assertWarns(BiopythonDeprecationWarning): - self.assertEqual(len(motif.instances), 21) - self.assertAlmostEqual(motif.instances[0].pvalue, 2.71e-12, places=14) - self.assertAlmostEqual(motif.instances[1].pvalue, 5.7e-12, places=13) - self.assertAlmostEqual(motif.instances[2].pvalue, 6.43e-12, places=14) - self.assertAlmostEqual(motif.instances[3].pvalue, 2.61e-11, places=13) - self.assertAlmostEqual(motif.instances[4].pvalue, 6.3e-11, places=12) - self.assertAlmostEqual(motif.instances[5].pvalue, 2.7e-10, places=11) - self.assertAlmostEqual(motif.instances[6].pvalue, 4.03e-10, places=12) - self.assertAlmostEqual(motif.instances[7].pvalue, 1.27e-09, places=11) - self.assertAlmostEqual(motif.instances[8].pvalue, 3.17e-09, places=11) - self.assertAlmostEqual(motif.instances[9].pvalue, 6.39e-09, places=11) - self.assertAlmostEqual(motif.instances[10].pvalue, 6.96e-09, places=11) - self.assertAlmostEqual(motif.instances[11].pvalue, 1.06e-08, places=10) - self.assertAlmostEqual(motif.instances[12].pvalue, 1.26e-08, places=10) - self.assertAlmostEqual(motif.instances[13].pvalue, 1.37e-08, places=10) - self.assertAlmostEqual(motif.instances[14].pvalue, 2.07e-08, places=10) - self.assertAlmostEqual(motif.instances[15].pvalue, 4.96e-08, places=10) - self.assertAlmostEqual(motif.instances[16].pvalue, 1.15e-07, places=9) - self.assertAlmostEqual(motif.instances[17].pvalue, 1.44e-07, places=9) - self.assertAlmostEqual(motif.instances[18].pvalue, 1.55e-07, places=9) - self.assertAlmostEqual(motif.instances[19].pvalue, 1.93e-07, places=9) - self.assertAlmostEqual(motif.instances[20].pvalue, 5.2e-07, places=8) - self.assertEqual(motif.instances[0].sequence_name, "RATRABGERB") - self.assertEqual(motif.instances[1].sequence_name, "BET2_YEAST") - self.assertEqual(motif.instances[2].sequence_name, "RATRABGERB") - self.assertEqual(motif.instances[3].sequence_name, "RATRABGERB") - self.assertEqual(motif.instances[4].sequence_name, "CAL1_YEAST") - self.assertEqual(motif.instances[5].sequence_name, "RAM1_YEAST") - self.assertEqual(motif.instances[6].sequence_name, "PFTB_RAT") - self.assertEqual(motif.instances[7].sequence_name, "RATRABGERB") - self.assertEqual(motif.instances[8].sequence_name, "BET2_YEAST") - self.assertEqual(motif.instances[9].sequence_name, "PFTB_RAT") - self.assertEqual(motif.instances[10].sequence_name, "RAM1_YEAST") - self.assertEqual(motif.instances[11].sequence_name, "CAL1_YEAST") - self.assertEqual(motif.instances[12].sequence_name, "PFTB_RAT") - self.assertEqual(motif.instances[13].sequence_name, "BET2_YEAST") - self.assertEqual(motif.instances[14].sequence_name, "RAM1_YEAST") - self.assertEqual(motif.instances[15].sequence_name, "RAM1_YEAST") - self.assertEqual(motif.instances[16].sequence_name, "RATRABGERB") - self.assertEqual(motif.instances[17].sequence_name, "RAM1_YEAST") - self.assertEqual(motif.instances[18].sequence_name, "PFTB_RAT") - self.assertEqual(motif.instances[19].sequence_name, "BET2_YEAST") - self.assertEqual(motif.instances[20].sequence_name, "CAL1_YEAST") - self.assertEqual(motif.instances[0].sequence_id, "sequence_3") - self.assertEqual(motif.instances[1].sequence_id, "sequence_2") - self.assertEqual(motif.instances[2].sequence_id, "sequence_3") - self.assertEqual(motif.instances[3].sequence_id, "sequence_3") - self.assertEqual(motif.instances[4].sequence_id, "sequence_4") - self.assertEqual(motif.instances[5].sequence_id, "sequence_0") - self.assertEqual(motif.instances[6].sequence_id, "sequence_1") - self.assertEqual(motif.instances[7].sequence_id, "sequence_3") - self.assertEqual(motif.instances[8].sequence_id, "sequence_2") - self.assertEqual(motif.instances[9].sequence_id, "sequence_1") - self.assertEqual(motif.instances[10].sequence_id, "sequence_0") - self.assertEqual(motif.instances[11].sequence_id, "sequence_4") - self.assertEqual(motif.instances[12].sequence_id, "sequence_1") - self.assertEqual(motif.instances[13].sequence_id, "sequence_2") - self.assertEqual(motif.instances[14].sequence_id, "sequence_0") - self.assertEqual(motif.instances[15].sequence_id, "sequence_0") - self.assertEqual(motif.instances[16].sequence_id, "sequence_3") - self.assertEqual(motif.instances[17].sequence_id, "sequence_0") - self.assertEqual(motif.instances[18].sequence_id, "sequence_1") - self.assertEqual(motif.instances[19].sequence_id, "sequence_2") - self.assertEqual(motif.instances[20].sequence_id, "sequence_4") - self.assertEqual(motif.instances[0].strand, "+") - self.assertEqual(motif.instances[1].strand, "+") - self.assertEqual(motif.instances[2].strand, "+") - self.assertEqual(motif.instances[3].strand, "+") - self.assertEqual(motif.instances[4].strand, "+") - self.assertEqual(motif.instances[5].strand, "+") - self.assertEqual(motif.instances[6].strand, "+") - self.assertEqual(motif.instances[7].strand, "+") - self.assertEqual(motif.instances[8].strand, "+") - self.assertEqual(motif.instances[9].strand, "+") - self.assertEqual(motif.instances[10].strand, "+") - self.assertEqual(motif.instances[11].strand, "+") - self.assertEqual(motif.instances[12].strand, "+") - self.assertEqual(motif.instances[13].strand, "+") - self.assertEqual(motif.instances[14].strand, "+") - self.assertEqual(motif.instances[15].strand, "+") - self.assertEqual(motif.instances[16].strand, "+") - self.assertEqual(motif.instances[17].strand, "+") - self.assertEqual(motif.instances[18].strand, "+") - self.assertEqual(motif.instances[19].strand, "+") - self.assertEqual(motif.instances[20].strand, "+") - self.assertEqual(motif.instances[0].length, 14) - self.assertEqual(motif.instances[1].length, 14) - self.assertEqual(motif.instances[2].length, 14) - self.assertEqual(motif.instances[3].length, 14) - self.assertEqual(motif.instances[4].length, 14) - self.assertEqual(motif.instances[5].length, 14) - self.assertEqual(motif.instances[6].length, 14) - self.assertEqual(motif.instances[7].length, 14) - self.assertEqual(motif.instances[8].length, 14) - self.assertEqual(motif.instances[9].length, 14) - self.assertEqual(motif.instances[10].length, 14) - self.assertEqual(motif.instances[11].length, 14) - self.assertEqual(motif.instances[12].length, 14) - self.assertEqual(motif.instances[13].length, 14) - self.assertEqual(motif.instances[14].length, 14) - self.assertEqual(motif.instances[15].length, 14) - self.assertEqual(motif.instances[16].length, 14) - self.assertEqual(motif.instances[17].length, 14) - self.assertEqual(motif.instances[18].length, 14) - self.assertEqual(motif.instances[19].length, 14) - self.assertEqual(motif.instances[20].length, 14) - self.assertEqual(motif.instances[0].start, 66) - self.assertEqual(motif.instances[1].start, 254) - self.assertEqual(motif.instances[2].start, 258) - self.assertEqual(motif.instances[3].start, 162) - self.assertEqual(motif.instances[4].start, 190) - self.assertEqual(motif.instances[5].start, 278) - self.assertEqual(motif.instances[6].start, 172) - self.assertEqual(motif.instances[7].start, 114) - self.assertEqual(motif.instances[8].start, 7) - self.assertEqual(motif.instances[9].start, 268) - self.assertEqual(motif.instances[10].start, 414) - self.assertEqual(motif.instances[11].start, 126) - self.assertEqual(motif.instances[12].start, 220) - self.assertEqual(motif.instances[13].start, 55) - self.assertEqual(motif.instances[14].start, 229) - self.assertEqual(motif.instances[15].start, 330) - self.assertEqual(motif.instances[16].start, 18) - self.assertEqual(motif.instances[17].start, 180) - self.assertEqual(motif.instances[18].start, 73) - self.assertEqual(motif.instances[19].start, 107) - self.assertEqual(motif.instances[20].start, 36) - self.assertEqual(motif.instances[0], "MNKEEILVFIKSCQ") - self.assertEqual(motif.instances[1], "INYEKLTEFILKCQ") - self.assertEqual(motif.instances[2], "IDREKLRSFILACQ") - self.assertEqual(motif.instances[3], "INVEKAIEFVLSCM") - self.assertEqual(motif.instances[4], "IDTEKLLGYIMSQQ") - self.assertEqual(motif.instances[5], "INVEKLLEWSSARQ") - self.assertEqual(motif.instances[6], "INREKLLQYLYSLK") - self.assertEqual(motif.instances[7], "INVDKVVAYVQSLQ") - self.assertEqual(motif.instances[8], "LLKEKHIRYIESLD") - self.assertEqual(motif.instances[9], "LNLKSLLQWVTSRQ") - self.assertEqual(motif.instances[10], "ENVRKIIHYFKSNL") - self.assertEqual(motif.instances[11], "LDKRSLARFVSKCQ") - self.assertEqual(motif.instances[12], "DLFEGTAEWIARCQ") - self.assertEqual(motif.instances[13], "FVKEEVISFVLSCW") - self.assertEqual(motif.instances[14], "ELTEGVLNYLKNCQ") - self.assertEqual(motif.instances[15], "FNKHALRDYILYCC") - self.assertEqual(motif.instances[16], "LLLEKHADYIASYG") - self.assertEqual(motif.instances[17], "IDRKGIYQWLISLK") - self.assertEqual(motif.instances[18], "LQREKHFHYLKRGL") - self.assertEqual(motif.instances[19], "DRKVRLISFIRGNQ") - self.assertEqual(motif.instances[20], "VNRMAIIFYSISGL") self.assertEqual(motif.consensus, "INKEKLIEYILSCQ") self.assertEqual(motif[3:-8].consensus, "EKL") @@ -5105,9 +3969,6 @@ def test_minimal_meme_parser(self): self.assertAlmostEqual(motif.evalue, 4.1e-09, places=10) self.assertEqual(motif.alphabet, "ACGT") self.assertIsNone(motif.alignment) - # using the old instances property: - with self.assertWarns(BiopythonDeprecationWarning): - self.assertIsNone(motif.instances) self.assertEqual(motif.consensus, "TGTGATCGAGGTCACACTT") self.assertEqual(motif.degenerate_consensus, "TGTGANNNWGNTCACAYWW") self.assertTrue( @@ -5181,9 +4042,6 @@ def test_minimal_meme_parser(self): ) ) self.assertEqual(motif[2:9].consensus, "CTGTATA") - # using the old instances property: - with self.assertWarns(BiopythonDeprecationWarning): - self.assertIsNone(motif.instances) with open("motifs/minimal_test.meme") as stream: record = motifs.parse(stream, "minimal") motif = record[2] @@ -5228,9 +4086,6 @@ def test_minimal_meme_parser(self): ) ) self.assertEqual(motif[2:9].consensus, "CTGTATA") - # using the old instances property: - with self.assertWarns(BiopythonDeprecationWarning): - self.assertIsNone(motif.instances) def test_meme_parser_rna(self): """Test if Bio.motifs can parse MEME output files using RNA.""" @@ -5253,9 +4108,6 @@ def test_meme_parser_rna(self): self.assertAlmostEqual(motif.evalue, 4.1e-09, places=10) self.assertEqual(motif.alphabet, "ACGU") self.assertIsNone(motif.alignment) - # using the old instances property: - with self.assertWarns(BiopythonDeprecationWarning): - self.assertIsNone(motif.instances) self.assertEqual(motif.consensus, "UGUGAUCGAGGUCACACUU") self.assertEqual(motif.degenerate_consensus, "UGUGANNNWGNUCACAYWW") self.assertTrue( @@ -5329,9 +4181,6 @@ def test_meme_parser_rna(self): ) ) self.assertEqual(motif[2:9].consensus, "CUGUAUA") - # using the old instances property: - with self.assertWarns(BiopythonDeprecationWarning): - self.assertIsNone(motif.instances) motif = record[2] self.assertEqual(motif.name, "IFXA_no_nsites_no_evalue_fake_RNA") @@ -5375,9 +4224,6 @@ def test_meme_parser_rna(self): ) ) self.assertEqual(motif[2:9].consensus, "CUGUAUA") - # using the old instances property: - with self.assertWarns(BiopythonDeprecationWarning): - self.assertIsNone(motif.instances) class TestMAST(unittest.TestCase):