Did I find the right examples for you? yes no

All Samples(12)  |  Call(6)  |  Derive(0)  |  Import(6)

src/c/o/cogent-1.5.3/cogent/align/pairwise.py   cogent(Download)
from indel_positions import leaf2pog
from cogent import LoadSeqs
from cogent.core.alignment import Aligned
from cogent.align.traceback import map_traceback
from cogent.util import parallel
    def __init__(self, leaf):
        _Alignable.__init__(self, leaf)
        if hasattr(leaf, 'sequence'):
            self.seq = leaf.sequence
            aligned = Aligned([(0, len(self.seq))], self.seq, len(self.seq))

src/p/y/pycogent-HEAD/cogent/align/pairwise.py   pycogent(Download)
from indel_positions import leaf2pog
from cogent import LoadSeqs
from cogent.core.alignment import Aligned
from cogent.align.traceback import map_traceback
from cogent.util import parallel
    def __init__(self, leaf):
        _Alignable.__init__(self, leaf)
        if hasattr(leaf, 'sequence'):
            self.seq = leaf.sequence
            aligned = Aligned([(0, len(self.seq))], self.seq, len(self.seq))

src/c/o/cogent-1.5.3/cogent/align/traceback.py   cogent(Download)
#!/usr/bin/env python
"""Conversion of dynamic program results ("arrays of arrows") into gap vectors,
gapped sequences or Cogent Alignment objects"""
 
from cogent.core.alignment import Alignment, Aligned
    aligneds = []
    for (start, end, amap, (name, seq)) in zip(starts, ends, maps, seqs):
        gs = Aligned(amap*word_length, seq[start*word_length:end*word_length])
        aligneds.append((name, gs))
    return Alignment(MolType=None, data=aligneds)

src/p/y/pycogent-HEAD/cogent/align/traceback.py   pycogent(Download)
#!/usr/bin/env python
"""Conversion of dynamic program results ("arrays of arrows") into gap vectors,
gapped sequences or Cogent Alignment objects"""
 
from cogent.core.alignment import Alignment, Aligned
    aligneds = []
    for (start, end, amap, (name, seq)) in zip(starts, ends, maps, seqs):
        gs = Aligned(amap*word_length, seq[start*word_length:end*word_length])
        aligneds.append((name, gs))
    return Alignment(MolType=None, data=aligneds)

src/c/o/cogent-1.5.3/cogent/db/ensembl/related_region.py   cogent(Download)
from pprint import pprint
import sqlalchemy as sql
 
from cogent import DNA
from cogent.core.alignment import SequenceCollection, Alignment, Aligned
 
        # we get the Seq objects to allow for copying of their annotations
        gapped_seq = Aligned(self.aln_map, seq)
 
        self._cached['AlignedSeq'] = gapped_seq

src/p/y/pycogent-HEAD/cogent/db/ensembl/related_region.py   pycogent(Download)
from pprint import pprint
import sqlalchemy as sql
 
from cogent import DNA
from cogent.core.alignment import SequenceCollection, Alignment, Aligned
 
        # we get the Seq objects to allow for copying of their annotations
        gapped_seq = Aligned(self.aln_map, seq)
 
        self._cached['AlignedSeq'] = gapped_seq