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src/e/e/eebprogramming-HEAD/lec10review/annotations.py   eebprogramming(Download)
exons = aln.getProjectedAnnotations('y', 'exon')
print exons
print aln.getSeq('y')[exons[0].map.withoutGaps()]
aln = LoadSeqs(data=[['x', '-AAAAAAAAA'], ['y', 'TTTT--TTTT']])
s = DNA.makeSequence("AAAAAAAAA", Name="x")

src/p/y/pycogent-HEAD/tests/test_core/test_maps.py   pycogent(Download)
    def test_getBySequenceAnnotation(self):
        aln = LoadSeqs(data={
                'a': 'ATCGAAATCGAT',
                'b': 'ATCGA--TCGAT'})
        b = aln.getSeq('b')

src/c/o/cogent-1.5.3/tests/test_core/test_maps.py   cogent(Download)
    def test_getBySequenceAnnotation(self):
        aln = LoadSeqs(data={
                'a': 'ATCGAAATCGAT',
                'b': 'ATCGA--TCGAT'})
        b = aln.getSeq('b')

src/q/i/qiime-1.8.0/tests/test_identify_chimeric_seqs.py   qiime(Download)
                  'reference_seqs_fp':self.reference_seqs_fp}
        self.bcc = BlastFragmentsChimeraChecker(params)
        s1 = test_seq_coll.getSeq('s1')
        actual = self.bcc._get_taxonomy(str(s1))
        expected = "Archaea;Euryarchaeota;Halobacteriales;uncultured"