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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

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

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

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

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
        s_in = 'AACA..CAU..CAGAUUUCCU..GGUGUAA.CGAA'
        s_out = 'AACA--CAU--CAGAUUUCCU--GGUGUAA-CGAA'
        sequence = ChangedSequence(s_in)
 
        self.assertEqual(sequence, s_out)
        s_in = '.' * 5
        s_out = '-' * 5
        sequence = ChangedSequence(s_in)
 
        self.assertEqual(sequence, s_out)
 
        # sequence of no blanks
        s_in = 'U' * 5
        s_out = 'U' * 5
        sequence = ChangedSequence(s_in)

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
        s_in = 'AACA..CAU..CAGAUUUCCU..GGUGUAA.CGAA'
        s_out = 'AACA--CAU--CAGAUUUCCU--GGUGUAA-CGAA'
        sequence = ChangedSequence(s_in)
 
        self.assertEqual(sequence, s_out)
        s_in = '.' * 5
        s_out = '-' * 5
        sequence = ChangedSequence(s_in)
 
        self.assertEqual(sequence, s_out)
 
        # sequence of no blanks
        s_in = 'U' * 5
        s_out = 'U' * 5
        sequence = ChangedSequence(s_in)

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