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src/c/o/cogent-1.5.3/cogent/app/infernal.py   cogent(Download)
from cogent.app.util import CommandLineApplication, ResultPath, get_tmp_filename
from cogent.parse.fasta import MinimalFastaParser
from cogent.parse.rfam import MinimalRfamParser, ChangedSequence, \
    ChangedRnaSequence, ChangedDnaSequence
from cogent.parse.infernal import CmsearchParser
    #get alignment and structure string from stockholm file.
    info, aln, structure_string = \
        list(MinimalRfamParser(open(stockholm_file_path,'U'),\
            seq_constructor=ChangedSequence))[0]
 
 
    info, aligned, struct_string = \
        list(MinimalRfamParser(res['Alignment'].readlines(),\
            seq_constructor=SEQ_CONSTRUCTOR_MAP[moltype]))[0]
 
 
    info, aligned, struct_string = \
        list(MinimalRfamParser(res['Alignment'].readlines(),\
            seq_constructor=SEQ_CONSTRUCTOR_MAP[moltype]))[0]
 

src/p/y/pycogent-HEAD/cogent/app/infernal.py   pycogent(Download)
from cogent.app.util import CommandLineApplication, ResultPath, get_tmp_filename
from cogent.parse.fasta import MinimalFastaParser
from cogent.parse.rfam import MinimalRfamParser, ChangedSequence, \
    ChangedRnaSequence, ChangedDnaSequence
from cogent.parse.infernal import CmsearchParser
    #get alignment and structure string from stockholm file.
    info, aln, structure_string = \
        list(MinimalRfamParser(open(stockholm_file_path,'U'),\
            seq_constructor=ChangedSequence))[0]
 
 
    info, aligned, struct_string = \
        list(MinimalRfamParser(res['Alignment'].readlines(),\
            seq_constructor=SEQ_CONSTRUCTOR_MAP[moltype]))[0]
 
 
    info, aligned, struct_string = \
        list(MinimalRfamParser(res['Alignment'].readlines(),\
            seq_constructor=SEQ_CONSTRUCTOR_MAP[moltype]))[0]
 

src/q/i/qiime-1.8.0/qiime/align_seqs.py   qiime(Download)
from cogent.app.util import ApplicationNotFoundError
from cogent.app.infernal import cmalign_from_alignment
from cogent.parse.rfam import MinimalRfamParser, ChangedSequence
import cogent.app.clustalw
import cogent.app.mafft
        # load template sequences
        try:
            info, template_alignment, struct = list(MinimalRfamParser(open(\
                self.Params['template_filepath'],'U'),\
                seq_constructor=ChangedSequence))[0]

src/q/i/qiime-HEAD/qiime/align_seqs.py   qiime(Download)
import brokit.mafft
 
from cogent.parse.rfam import MinimalRfamParser, ChangedSequence
from skbio.app.util import ApplicationNotFoundError
from skbio.core.exception import RecordError
        # load template sequences
        try:
            info, template_alignment, struct = list(MinimalRfamParser(open(
                self.Params['template_filepath'], 'U'),
                seq_constructor=ChangedSequence))[0]

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
        # you expect to get back as much information as possible, also
        # half records or sequences
        result = MinimalRfamParser(self._fake_record_bad_sequence_1,strict=False)
        self.assertEqual(len(list(MinimalRfamParser(\
            self._fake_record_bad_sequence_1,strict=False))[0][1].NamedSeqs), 3)            
 
        data = []
        for r in MinimalRfamParser(self._fake_two_records, strict=False):
            data.append(r)
        self.assertEqual(data[0],(headers,sequences,structure))

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
        # you expect to get back as much information as possible, also
        # half records or sequences
        result = MinimalRfamParser(self._fake_record_bad_sequence_1,strict=False)
        self.assertEqual(len(list(MinimalRfamParser(\
            self._fake_record_bad_sequence_1,strict=False))[0][1].NamedSeqs), 3)            
 
        data = []
        for r in MinimalRfamParser(self._fake_two_records, strict=False):
            data.append(r)
        self.assertEqual(data[0],(headers,sequences,structure))

src/p/y/pycogent-HEAD/tests/test_app/test_infernal.py   pycogent(Download)
    cmalign_from_alignment, cmalign_from_file, cmsearch_from_alignment,\
    cmsearch_from_file
from cogent.parse.rfam import MinimalRfamParser, ChangedRnaSequence, \
    ChangedSequence
from cogent.format.stockholm import stockholm_from_alignment

src/c/o/cogent-1.5.3/tests/test_app/test_infernal.py   cogent(Download)
    cmalign_from_alignment, cmalign_from_file, cmsearch_from_alignment,\
    cmsearch_from_file
from cogent.parse.rfam import MinimalRfamParser, ChangedRnaSequence, \
    ChangedSequence
from cogent.format.stockholm import stockholm_from_alignment