def test_snv_prot_change_annotator():
'It test the snv_prot_changepolia annotator'
# first annotate orf
seq = 'ATGGCTTCATCCATTCTCTCATCCGCCGNTGTGGCCTTTGNCAACAGGGCTTCCCCTGCTCA'
seq += 'AGCTAGCATGGGGGCACCATTCACTGGCCTAAAATCCGCCGCTGCTTTCCCNGTTTTATGTA'
seq += 'CTGTTTTNACTCGCANGACCAACGACATCACCACTTTGGTTAGCAATGGGGGAAGAGTTCAG'
seq += 'GGCNTGAAGGTGTGCCCACCACTTGGATTGAAGAAGTTCGAGACTCTTTCTTACCTTCCTGA'
seq += 'TATGAGTAACGAGCAATTGGGAAAGGAAGTTGACTACCTTCTCAGGAAGGGATGGATTCCCT'
seq += 'GCATTGAATTCGACATTCACAGTGGATTCGTTTACCGTGAGACCCACAGGTCACCAGGATAC'
seq += 'TTCGATGGACGCTACTGGACCATGTGGAAGCTGCCCATGTTTGGCTGCACCGAT'
orf = 'ATGGCTTCATCCATTCTCTCATCCGCCGNTGTGGCCTTTGNCAACAGGGCTTCCCTGCTCAA'
orf += 'GCTAGCATGGGGGCACCATTCACTGGCCTAAAATCCGCCGCTGCTTTCCCNGTNACTCGCAN'
orf += 'GACCAACGACATCACCACTTTGGTTAGCAATGGGGGAAGAGTTCAGGGCNTGAAGGTGTGCC'
orf += 'CACCACTTGGATTGAAGAAGTTCGAGACTCTTTCTTACCTTCCTGATATGAGTAACGAGCAA'
orf += 'TTGGGAAAGGAAGTTGACTACCTTCTCAGGAAGGGATGGATTCCCTGCATTGAATTCGACAT'
orf += 'TCACAGTGGATTCGTTTACCGTGAGACCCACAGGTCACCAGGATACTTCGATGGACGCTAC'
orf += 'TGGACCATGTGGAAGCTGCCCATGTTTGGCTGCACCGAT'
qualifiers = {'strand':'forward', 'dna':Seq(orf), 'prot':'prot'}
feature = SeqFeature(location=FeatureLocation(0, len(seq)), type='orf',
qualifiers=qualifiers)
alleles = {('A', SNP): None, ('G', INVARIANT):None}
snv = SeqFeature(location=FeatureLocation(24, 24), type='snv',
qualifiers = {'alleles':alleles})
alleles = {('A', SNP): None, ('T', INVARIANT):None}
snv2 = SeqFeature(location=FeatureLocation(56, 56), type='snv',
qualifiers = {'alleles':alleles})
alleles = {('T', SNP): None, ('A', INVARIANT):None}
snv3 = SeqFeature(location=FeatureLocation(399, 399), type='snv',
qualifiers = {'alleles':alleles})
alleles = {('T', INVARIANT):None, ('AG', INSERTION):None}
snv4 = SeqFeature(location=FeatureLocation(250, 250), type='snv',
qualifiers = {'alleles':alleles})
alleles = {('G', INVARIANT):None, ('--', DELETION):None}
snv5 = SeqFeature(location=FeatureLocation(251, 251), type='snv',
qualifiers = {'alleles':alleles})
sequence = SeqWithQuality(seq=Seq(seq), name='query')
#print str(sequence[257:265].seq)
#print sequence[256]
sequence.features = [feature, snv, snv2, snv3, snv4, snv5]
annotator = create_prot_change_annotator()
annotator(sequence)
[feature, snv, snv2, snv3, snv4, snv5] = sequence.features
assert snv.qualifiers['protein_change']['kind'] == 'substitution'
assert snv3.qualifiers['protein_change']['kind'] == 'substitution'
assert snv4.qualifiers['protein_change']['kind'] == 'breakage'
#
assert snv.qualifiers['protein_change']['location'] == 'codon_1'
def test_remove_annotations():
'It test ermove annotations from seq_with quality'
seq = SeqWithQuality(Seq('actg'), qual=[30, 30, 30, 30])
seq.description = 'Description'
annotations = {'arabidopsis-orthologs':'justone',
'GOs':'GO12345',
}
snv = SeqFeature(location=FeatureLocation(4, 4), type='snv')
intron = SeqFeature(location=FeatureLocation(4, 4), type='intron')
orf = SeqFeature(location=FeatureLocation(4, 4), type='orf')
ssr = SeqFeature(location=FeatureLocation(4, 4), type='microsatellite')
features = [snv, intron, orf, ssr]
seq.annotations = annotations
seq.features = features
seq.remove_annotations('GOs')
seq.remove_annotations('orthologs')
assert seq.annotations == {}
seq.remove_annotations('snv')
seq.remove_annotations('intron')
seq.remove_annotations('microsatellite')
seq.remove_annotations('orf')
seq.remove_annotations('description')
assert seq.features == []
assert seq.description == UNKNOWN_DESCRIPTION
# remome snv filters
seq = SeqWithQuality(Seq('actg'), qual=[30, 30, 30, 30])
seq.description = 'Description'
filters = {'not_intron':True, 'puff':False}
snv = SeqFeature(location=FeatureLocation(4, 4), type='snv',
qualifiers={'alleles':'alleles',
'filters':filters})
seq.features = [snv]
seq.remove_annotations('snv_filters')
assert seq.features[0].qualifiers['filters'] == {}
assert seq.features[0].qualifiers['alleles'] == 'alleles'
