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src/c/o/cogent-1.5.3/cogent/app/rnaalifold.py   cogent(Download)
from cogent.core.moltype import RNA
from cogent.parse.fasta import MinimalFastaParser
from cogent.parse.rnaalifold import rnaalifold_parser, MinimalRnaalifoldParser
from cogent.format.clustal import clustal_from_alignment
from cogent.struct.rna2d import ViennaStructure
 
    #seq,pairs,energy = rnaalifold_parser(res['StdOut'].readlines())
    pairs_list = MinimalRnaalifoldParser(res['StdOut'].readlines())
 
    res.cleanUp()

src/p/y/pycogent-HEAD/cogent/app/rnaalifold.py   pycogent(Download)
from cogent.core.moltype import RNA
from cogent.parse.fasta import MinimalFastaParser
from cogent.parse.rnaalifold import rnaalifold_parser, MinimalRnaalifoldParser
from cogent.format.clustal import clustal_from_alignment
from cogent.struct.rna2d import ViennaStructure
 
    #seq,pairs,energy = rnaalifold_parser(res['StdOut'].readlines())
    pairs_list = MinimalRnaalifoldParser(res['StdOut'].readlines())
 
    res.cleanUp()

src/c/o/cogent-1.5.3/cogent/app/vienna_package.py   cogent(Download)
from cogent.struct.rna2d import ViennaStructure
from cogent.core.alignment import DataError
from cogent.parse.rnaalifold import MinimalRnaalifoldParser
from random import choice
 
    res = app([sequence,constraint_string])
    #Parse out seq, struct string and energy.
    seq, struct, energy = MinimalRnaalifoldParser(res['StdOut'].readlines())[0]
    #Clean up after application.
    res.cleanUp()
 
    #Parse out seq, struct string and energy.
    seq, struct, energy = MinimalRnaalifoldParser(res['StdOut'].readlines())[0]
    #Clean up after application.
    res.cleanUp()

src/p/y/pycogent-HEAD/cogent/app/vienna_package.py   pycogent(Download)
from cogent.struct.rna2d import ViennaStructure
from cogent.core.alignment import DataError
from cogent.parse.rnaalifold import MinimalRnaalifoldParser
from random import choice
 
    res = app([sequence,constraint_string])
    #Parse out seq, struct string and energy.
    seq, struct, energy = MinimalRnaalifoldParser(res['StdOut'].readlines())[0]
    #Clean up after application.
    res.cleanUp()
 
    #Parse out seq, struct string and energy.
    seq, struct, energy = MinimalRnaalifoldParser(res['StdOut'].readlines())[0]
    #Clean up after application.
    res.cleanUp()

src/p/y/pycogent-HEAD/tests/test_parse/test_rnaalifold.py   pycogent(Download)
#!/usr/bin/env python
 
from cogent.util.unit_test import TestCase, main
from cogent.core.info import Info
from cogent.parse.rnaalifold import rnaalifold_parser, MinimalRnaalifoldParser
 
        #Test one structure
        obs = MinimalRnaalifoldParser(self.rnaalifold_out)
        self.assertEqual(obs,self.rnaalifold_exp)
 
        #Test two structures
        obs_2 = MinimalRnaalifoldParser(self.rnaalifold_out_2)

src/c/o/cogent-1.5.3/tests/test_parse/test_rnaalifold.py   cogent(Download)
#!/usr/bin/env python
 
from cogent.util.unit_test import TestCase, main
from cogent.core.info import Info
from cogent.parse.rnaalifold import rnaalifold_parser, MinimalRnaalifoldParser
 
        #Test one structure
        obs = MinimalRnaalifoldParser(self.rnaalifold_out)
        self.assertEqual(obs,self.rnaalifold_exp)
 
        #Test two structures
        obs_2 = MinimalRnaalifoldParser(self.rnaalifold_out_2)