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src/c/o/cogent-1.5.3/cogent/parse/cmfinder.py   cogent(Download)
#!/usr/bin/env python
 
from cogent.util.transform import make_trans
from cogent.struct.rna2d   import wuss_to_vienna, Pairs
from cogent.parse.rfam     import RfamParser
    Parser tested through RfamParser test
    """
    for info, alignment, struct in RfamParser(lines,strict=False):
        struct = wuss_to_vienna(struct)
        pairs = struct.toPairs()

src/p/y/pycogent-HEAD/cogent/parse/cmfinder.py   pycogent(Download)
#!/usr/bin/env python
 
from cogent.util.transform import make_trans
from cogent.struct.rna2d   import wuss_to_vienna, Pairs
from cogent.parse.rfam     import RfamParser
    Parser tested through RfamParser test
    """
    for info, alignment, struct in RfamParser(lines,strict=False):
        struct = wuss_to_vienna(struct)
        pairs = struct.toPairs()

src/c/o/cogent-1.5.3/tests/test_parse/test_rfam.py   cogent(Download)
"""
 
from cogent.parse.rfam import is_header_line, is_seq_line, is_structure_line,\
HeaderToInfo, MinimalRfamParser, RfamFinder, NameToInfo, RfamParser,\
ChangedSequence, is_empty_or_html
        '.>>>>>....<<<<<<<<<<.....>>>>>>>>>>..'])            
 
        for r in RfamParser(self._fake_record):
            headers,sequences,structure = r
 
 
        # strict = False
        x =  list(RfamParser(self._fake_record_bad_header_1, strict=False))
        obs = list(RfamParser(self._fake_record_bad_header_1,\
            strict=False))[0][0].keys()
            'AUGGGAAACUCCCCCUCCUAUAACCCCCCCGCUGGCAUCUCCCCCUCAGACUGGC'}
        exp_struct = '<<<<<<.........>>>>>>.........<<<<<<.............>>>>>>'
        h, a, s = list(RfamParser(self.single_family))[0]
        self.assertEqual(h,exp_header)
        self.assertEqual(a,exp_aln)

src/p/y/pycogent-HEAD/tests/test_parse/test_rfam.py   pycogent(Download)
"""
 
from cogent.parse.rfam import is_header_line, is_seq_line, is_structure_line,\
HeaderToInfo, MinimalRfamParser, RfamFinder, NameToInfo, RfamParser,\
ChangedSequence, is_empty_or_html
        '.>>>>>....<<<<<<<<<<.....>>>>>>>>>>..'])            
 
        for r in RfamParser(self._fake_record):
            headers,sequences,structure = r
 
 
        # strict = False
        x =  list(RfamParser(self._fake_record_bad_header_1, strict=False))
        obs = list(RfamParser(self._fake_record_bad_header_1,\
            strict=False))[0][0].keys()
            'AUGGGAAACUCCCCCUCCUAUAACCCCCCCGCUGGCAUCUCCCCCUCAGACUGGC'}
        exp_struct = '<<<<<<.........>>>>>>.........<<<<<<.............>>>>>>'
        h, a, s = list(RfamParser(self.single_family))[0]
        self.assertEqual(h,exp_header)
        self.assertEqual(a,exp_aln)