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src/c/o/cogent-1.5.3/tests/test_parse/test_bpseq.py   cogent(Download)
from cogent.core.info import Info
from cogent.struct.knots import inc_order
from cogent.parse.bpseq import BpseqParseError, construct_sequence,\
    parse_header, parse_residues, MinimalBpseqParser, BpseqParser,\
    bpseq_specify_output
        exp_seq = 'CAGACU'
        exp_pairs = [(1,5),(2,4)]
        obs_seq, obs_pairs = BpseqParser(lines, num_base=3,\
            unpaired_symbol='xxx')
        self.assertEqual(obs_seq, exp_seq)
        #skips lines in unknown format
        lines = RES_LINES_UNKNOWN.split('\n')
        obs_seq, obs_pairs = BpseqParser(lines)
 
        self.assertEqual(obs_seq, exp_seq)

src/p/y/pycogent-HEAD/tests/test_parse/test_bpseq.py   pycogent(Download)
from cogent.core.info import Info
from cogent.struct.knots import inc_order
from cogent.parse.bpseq import BpseqParseError, construct_sequence,\
    parse_header, parse_residues, MinimalBpseqParser, BpseqParser,\
    bpseq_specify_output
        exp_seq = 'CAGACU'
        exp_pairs = [(1,5),(2,4)]
        obs_seq, obs_pairs = BpseqParser(lines, num_base=3,\
            unpaired_symbol='xxx')
        self.assertEqual(obs_seq, exp_seq)
        #skips lines in unknown format
        lines = RES_LINES_UNKNOWN.split('\n')
        obs_seq, obs_pairs = BpseqParser(lines)
 
        self.assertEqual(obs_seq, exp_seq)