def test_repr():
'It test the repr reader'
assert u'a (h)' == _cast_to_class("u'a (h)'")
assert ('adios',) == _cast_to_class("('adios',)")
assert ['arab1', 'arab2'] == _cast_to_class("['arab1', 'arab2']")
assert ('arab1', 'arab2') == _cast_to_class("('arab1', 'arab2')")
result = _cast_to_class("{1: 2}")
assert {1: 2} == result
assert {'al': {'c': 1}, 'T': 2} == _cast_to_class("{'al': {'c': 1}, 'T': 2}")
seq1 = SeqWithQuality(seq=Seq('ATCT'))
seq2 = SeqWithQuality(seq=Seq('AAAA'))
fcontent = repr(seq1) + '\n' + repr(seq2) + '\n'
fhand = StringIO.StringIO(fcontent)
seqs = list(seqs_in_file(fhand, format='repr'))
assert repr(seqs[0]) == repr(seq1)
assert repr(seqs[1]) == repr(seq2)
#with quality
seq1 = SeqWithQuality(seq=Seq('ATCT'), qual=[10, 2, 3, 4])
fcontent = repr(seq1) + '\n'
fhand = StringIO.StringIO(fcontent)
seqs = list(seqs_in_file(fhand, format='repr'))
assert repr(seqs[0]) == repr(seq1)
#a seq with features
seq1 = SeqWithQuality(seq=Seq('GAAAAGATGTG', SingleLetterAlphabet()),
id='seq', name='seq', description='', dbxrefs=[],
features=[SeqFeature(FeatureLocation(ExactPosition(478),
ExactPosition(478)),
type='intron',
qualifiers={'db': 'tomato'} ),
SeqFeature(FeatureLocation(ExactPosition(572),
ExactPosition(572)),
type='intron',
qualifiers={'db': 'tomato'} )],
annotations={}, qual=None)
fcontent = repr(seq1) + '\n'
fhand = StringIO.StringIO(fcontent)
seq0 = list(seqs_in_file(fhand, format='repr'))[0]
assert seq0.seq == seq1.seq
assert seq0.qual == seq1.qual
assert seq0.description == seq1.description
assert seq0.annotations == seq1.annotations
feat0 = seq0.features[0]
feat1 = seq1.features[0]
assert feat0.type == feat1.type
assert feat0.qualifiers == feat1.qualifiers
assert str(feat0.location) == str(feat1.location)
#some more qualifiers
fhand = tempfile.NamedTemporaryFile(suffix='.repr')
seq1 = SeqWithQuality(id='seqid', name='seqname',
description='seqdescription', seq=Seq('ATGAT'))
seq1.letter_annotations["phred_quality"] = [40, 40, 38, 30, 30]
seq1.annotations['source'] = 'ara1'
seqfeature = SeqFeature(location=FeatureLocation(5, 8),
type='orthologs',
qualifiers={'arabidposis':['arab1', 'arab2']})
seq1.features.append(seqfeature)
fcontent = repr(seq1) + '\n'
fhand = StringIO.StringIO(fcontent)
seq0 = list(seqs_in_file(fhand, format='repr'))[0]
assert seq0.seq == seq1.seq
assert seq0.qual == seq1.qual
assert seq0.description == seq1.description
assert seq0.annotations == seq1.annotations
feat0 = seq0.features[0]
feat1 = seq1.features[0]
assert feat0.type == feat1.type
assert feat0.qualifiers == feat1.qualifiers
assert str(feat0.location) == str(feat1.location)
#with snps
repr_ = "SeqWithQuality(seq=Seq('GGGGATTTG', Alphabet()), features=[SeqFeature(FeatureLocation(ExactPosition(213),ExactPosition(213)), type='snv', qualifiers={'alleles': {('C', 3): {'read_groups': ['group1+454', 'group1+454', 'group1+454'], 'qualities': [44.0, 44.0, 44.0], 'libraries': ['group1', 'group1', 'group1'], 'read_names': ['seq1', 'seq4', 'seq7'], 'orientations': [True, True, True], 'samples': ['group1+454', 'group1+454', 'group1+454'], 'quality': 66.0, 'mapping_qualities': [149, 149, 149]}, ('T', 0): {'read_groups': ['group1+454', 'group1+454', 'group1+454', 'group1+454', 'group1+454', 'group1+454'], 'qualities': [44.0, 44.0, 44.0, 44.0, 44.0, 44.0], 'libraries': ['group1', 'group1', 'group1', 'group1', 'group1', 'group1'], 'read_names': ['seq2', 'seq3', 'seq5', 'seq6', 'seq8', 'seq9'], 'orientations': [True, True, True, True, True, True], 'samples': ['group1+454', 'group1+454', 'group1+454', 'group1+454', 'group1+454', 'group1+454'], 'quality': 66.0, 'mapping_qualities': [28, 28, 28, 28, 28, 28]}}, 'reference_allele': 'C'} )])\n"
alleles = {('C', 3):
{'read_groups': ['group1+454', 'group1+454', 'group1+454'],
'qualities': [44.0, 44.0, 44.0],
'libraries': ['group1', 'group1', 'group1'],
'read_names': ['seq1', 'seq4', 'seq7'],
'orientations': [True, True, True],
'samples': ['group1+454', 'group1+454', 'group1+454'],
'quality': 66.0, 'mapping_qualities': [149, 149, 149]},
('T', 0):
{'read_groups': ['group1+454', 'group1+454', 'group1+454',
'group1+454', 'group1+454', 'group1+454'],
'qualities': [44.0, 44.0, 44.0, 44.0, 44.0, 44.0],
'libraries': ['group1', 'group1', 'group1', 'group1',
'group1', 'group1'],
'read_names': ['seq2', 'seq3', 'seq5', 'seq6', 'seq8',
'seq9'],
'orientations': [True, True, True, True, True, True],
'samples': ['group1+454', 'group1+454', 'group1+454',
'group1+454', 'group1+454', 'group1+454'],
'quality': 66.0,
'mapping_qualities': [28, 28, 28, 28, 28, 28]}
}
fcontent = repr_
fhand = StringIO.StringIO(fcontent)
seq0 = list(seqs_in_file(fhand, format='repr'))[0]
alleles0 = seq0.features[0].qualifiers['alleles']
assert alleles == alleles0