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src/c/o/cogent-1.5.3/cogent/parse/stockholm.py   cogent(Download)
from cogent.parse.record import RecordError
from cogent.parse.record_finder import DelimitedRecordFinder
from cogent.parse.clustal import ClustalParser
from cogent.core.sequence import RnaSequence as Rna
from cogent.core.sequence import ProteinSequence as Protein
def load_from_clustal(data, seq_constructor=Sequence, strict=True,gap_char='-'):
    recs=[(name, seq_constructor(seq.replace('.',gap_char), )) for name, seq in\
        ClustalParser(data, strict)]
    lengths = [len(i[1]) for i in recs]
    if lengths and max(lengths) == min(lengths):

src/c/o/cogent-1.5.3/cogent/parse/rfam.py   cogent(Download)
from cogent.parse.record import RecordError
from cogent.parse.record_finder import DelimitedRecordFinder
from cogent.parse.clustal import ClustalParser
from cogent.core.sequence import RnaSequence as Rna
from cogent.core.sequence import DnaSequence as Dna
def load_from_clustal(data, seq_constructor=Sequence, strict=True):
    recs = [(name, seq_constructor(seq, )) for name, seq in\
        ClustalParser(data, strict)]
    lengths = [len(i[1]) for i in recs]
    if lengths and max(lengths) == min(lengths):

src/p/y/pycogent-HEAD/cogent/parse/stockholm.py   pycogent(Download)
from cogent.parse.record import RecordError
from cogent.parse.record_finder import DelimitedRecordFinder
from cogent.parse.clustal import ClustalParser
from cogent.core.sequence import RnaSequence as Rna
from cogent.core.sequence import ProteinSequence as Protein
def load_from_clustal(data, seq_constructor=Sequence, strict=True,gap_char='-'):
    recs=[(name, seq_constructor(seq.replace('.',gap_char), )) for name, seq in\
        ClustalParser(data, strict)]
    lengths = [len(i[1]) for i in recs]
    if lengths and max(lengths) == min(lengths):

src/p/y/pycogent-HEAD/cogent/parse/rfam.py   pycogent(Download)
from cogent.parse.record import RecordError
from cogent.parse.record_finder import DelimitedRecordFinder
from cogent.parse.clustal import ClustalParser
from cogent.core.sequence import RnaSequence as Rna
from cogent.core.sequence import DnaSequence as Dna
def load_from_clustal(data, seq_constructor=Sequence, strict=True):
    recs = [(name, seq_constructor(seq, )) for name, seq in\
        ClustalParser(data, strict)]
    lengths = [len(i[1]) for i in recs]
    if lengths and max(lengths) == min(lengths):

src/c/o/cogent-1.5.3/cogent/app/clustalw.py   cogent(Download)
from cogent.core.alignment import SequenceCollection, Alignment
from cogent.parse.tree import DndParser 
from cogent.parse.clustal import ClustalParser
from cogent.core.tree import PhyloNode
from cogent.core.moltype import RNA, DNA, PROTEIN
    res = app(int_map.toFasta())
    #Get alignment as dict out of results
    alignment = dict(ClustalParser(res['Align'].readlines()))
    #Make new dict mapping original IDs
    new_alignment = {}
 
    #Get alignment as dict out of results
    alignment = dict(ClustalParser(res['Align'].readlines()))
 
    #Make new dict mapping original IDs
 
    #Get alignment as dict out of results
    alignment = dict(ClustalParser(res['Align'].readlines()))
 
    #Make new dict mapping original IDs

src/p/y/pycogent-HEAD/cogent/app/clustalw.py   pycogent(Download)
from cogent.core.alignment import SequenceCollection, Alignment
from cogent.parse.tree import DndParser 
from cogent.parse.clustal import ClustalParser
from cogent.core.tree import PhyloNode
from cogent.core.moltype import RNA, DNA, PROTEIN
    res = app(int_map.toFasta())
    #Get alignment as dict out of results
    alignment = dict(ClustalParser(res['Align'].readlines()))
    #Make new dict mapping original IDs
    new_alignment = {}
 
    #Get alignment as dict out of results
    alignment = dict(ClustalParser(res['Align'].readlines()))
 
    #Make new dict mapping original IDs
 
    #Get alignment as dict out of results
    alignment = dict(ClustalParser(res['Align'].readlines()))
 
    #Make new dict mapping original IDs

src/p/y/pycogent-HEAD/tests/test_align/test_weights/test_methods.py   pycogent(Download)
from cogent.util.unit_test import TestCase, main
from cogent.parse.tree import DndParser
from cogent.parse.clustal import ClustalParser as MinimalClustalParser
from cogent.core.alignment import Alignment
from cogent.core.profile import Profile
def ClustalParser(f):
    return Alignment(list(MinimalClustalParser(f)))
 
class GeneralTests(TestCase):
    """General tests for all classes in this file, provides general setup"""

src/c/o/cogent-1.5.3/tests/test_align/test_weights/test_methods.py   cogent(Download)
from cogent.util.unit_test import TestCase, main
from cogent.parse.tree import DndParser
from cogent.parse.clustal import ClustalParser as MinimalClustalParser
from cogent.core.alignment import Alignment
from cogent.core.profile import Profile
def ClustalParser(f):
    return Alignment(list(MinimalClustalParser(f)))
 
class GeneralTests(TestCase):
    """General tests for all classes in this file, provides general setup"""