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src/c/o/cogent-1.5.3/cogent/parse/stockholm.py   cogent(Download)
from cogent.core.moltype import BYTES
from cogent.core.info import Info
from cogent.struct.rna2d import WussStructure
from cogent.util.transform import trans_all,keep_chars
from cogent.core.alignment import Alignment, DataError, SequenceCollection

src/c/o/cogent-1.5.3/cogent/parse/rfam.py   cogent(Download)
from cogent.core.moltype import BYTES
from cogent.core.info import Info
from cogent.struct.rna2d import WussStructure
from cogent.util.transform import trans_all,keep_chars
from cogent.core.alignment import Alignment, DataError, SequenceCollection

src/p/y/pycogent-HEAD/cogent/parse/stockholm.py   pycogent(Download)
from cogent.core.moltype import BYTES
from cogent.core.info import Info
from cogent.struct.rna2d import WussStructure
from cogent.util.transform import trans_all,keep_chars
from cogent.core.alignment import Alignment, DataError, SequenceCollection

src/p/y/pycogent-HEAD/cogent/parse/rfam.py   pycogent(Download)
from cogent.core.moltype import BYTES
from cogent.core.info import Info
from cogent.struct.rna2d import WussStructure
from cogent.util.transform import trans_all,keep_chars
from cogent.core.alignment import Alignment, DataError, SequenceCollection

src/c/o/cogent-1.5.3/tests/test_struct/test_rna2d.py   cogent(Download)
#!/usr/bin/env python
"""Tests for ViennaStructure and related classes.
"""
from cogent.util.unit_test import TestCase, main
from cogent.struct.rna2d import ViennaStructure, Vienna, Pairs,\
        self.Struct = WussStructure
        super(WussStructureTests,self).setUp()
        self.WussNoPairs = WussStructure('.-_,~:')
        self.WussOneHelix = WussStructure('[-{<(__)-->}]',-0.01)
        self.WussTwoHelix = WussStructure('{[.]}(<>).',1.11)
        self.WussThreeHelix = WussStructure('::(<<({__}),,([(__)])-->>)')

src/p/y/pycogent-HEAD/tests/test_struct/test_rna2d.py   pycogent(Download)
#!/usr/bin/env python
"""Tests for ViennaStructure and related classes.
"""
from cogent.util.unit_test import TestCase, main
from cogent.struct.rna2d import ViennaStructure, Vienna, Pairs,\
        self.Struct = WussStructure
        super(WussStructureTests,self).setUp()
        self.WussNoPairs = WussStructure('.-_,~:')
        self.WussOneHelix = WussStructure('[-{<(__)-->}]',-0.01)
        self.WussTwoHelix = WussStructure('{[.]}(<>).',1.11)
        self.WussThreeHelix = WussStructure('::(<<({__}),,([(__)])-->>)')

src/p/y/pycogent-HEAD/tests/test_parse/test_stockholm.py   pycogent(Download)
from cogent.parse.record import RecordError
from cogent.core.info import Info
from cogent.struct.rna2d import WussStructure
from cogent.core.alignment import Alignment
from cogent.core.moltype import BYTES
            'AGCAAGUUUGAUCCCGACCCGU--AGGGCCGGGAUUU'])}
 
        structure = WussStructure(''.join(\
        ['...<<<<<<<.....>>>>>>>....................<<<<<...',\
        '.>>>>>....<<<<<<<<<<.....>>>>>>>>>>..']))

src/p/y/pycogent-HEAD/tests/test_parse/test_rfam.py   pycogent(Download)
from cogent.parse.record import RecordError
from cogent.core.info import Info
from cogent.struct.rna2d import WussStructure
from cogent.core.alignment import Alignment
from cogent.core.moltype import BYTES
            'AGCAAGUUUGAUCCCGACCCGU--AGGGCCGGGAUUU'])}
 
        structure = WussStructure(''.join(\
        ['...<<<<<<<.....>>>>>>>....................<<<<<...',\
        '.>>>>>....<<<<<<<<<<.....>>>>>>>>>>..']))

src/c/o/cogent-1.5.3/tests/test_parse/test_stockholm.py   cogent(Download)
from cogent.parse.record import RecordError
from cogent.core.info import Info
from cogent.struct.rna2d import WussStructure
from cogent.core.alignment import Alignment
from cogent.core.moltype import BYTES
            'AGCAAGUUUGAUCCCGACCCGU--AGGGCCGGGAUUU'])}
 
        structure = WussStructure(''.join(\
        ['...<<<<<<<.....>>>>>>>....................<<<<<...',\
        '.>>>>>....<<<<<<<<<<.....>>>>>>>>>>..']))

src/c/o/cogent-1.5.3/tests/test_parse/test_rfam.py   cogent(Download)
from cogent.parse.record import RecordError
from cogent.core.info import Info
from cogent.struct.rna2d import WussStructure
from cogent.core.alignment import Alignment
from cogent.core.moltype import BYTES
            'AGCAAGUUUGAUCCCGACCCGU--AGGGCCGGGAUUU'])}
 
        structure = WussStructure(''.join(\
        ['...<<<<<<<.....>>>>>>>....................<<<<<...',\
        '.>>>>>....<<<<<<<<<<.....>>>>>>>>>>..']))