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src/c/o/cogent-1.5.3/cogent/db/ensembl/region.py   cogent(Download)
import sys
import sqlalchemy as sql
 
from cogent import DNA
from cogent.core.annotation import Feature

src/p/y/pycogent-HEAD/cogent/db/ensembl/region.py   pycogent(Download)
import sys
import sqlalchemy as sql
 
from cogent import DNA
from cogent.core.annotation import Feature

src/c/o/cogent-1.5.3/cogent/parse/genbank.py   cogent(Download)
from string import maketrans, strip, rstrip
from cogent.core.moltype import PROTEIN, DNA, ASCII
from cogent.core.annotation import Feature
from cogent.core.info import Info
 

src/p/y/pycogent-HEAD/cogent/parse/genbank.py   pycogent(Download)
from string import maketrans, strip, rstrip
from cogent.core.moltype import PROTEIN, DNA, ASCII
from cogent.core.annotation import Feature
from cogent.core.info import Info
 

src/e/e/eebprogramming-HEAD/lec10review/annotations.py   eebprogramming(Download)
#!/usr/bin/env python
# taken from http://pycogent.sourceforge.net/
from cogent import DNA
from cogent.core.annotation import Feature
s = DNA.makeSequence("AAGAAGAAGACCCCCAAAAAAAAAATTTTTTTTTTAAAAAAAAAAAAA", Name="Orig")

src/e/e/eebprogramming-HEAD/lec10review/2annotations.py   eebprogramming(Download)
exon1 = s.addFeature('exon', 'exon1', [(10,15)])
exon2 = s.addFeature('exon', 'exon2', [(30,40)])
from cogent.core.annotation import Feature
s2=DNA.makeSequence("aagaagaagacccccaaaaaaaaaattttttttttaaaaaaaaaaaaa", Name="Orig2")
exon3 = s2.addAnnotation(Feature, 'exon', 'exon1', [(35,40)])

src/c/o/cogent-1.5.3/tests/test_core/test_maps.py   cogent(Download)
#!/usr/bin/env python
 
import unittest
from cogent.core.location import Map, Span
from cogent.core.annotation import _Annotatable, Feature, _Feature
def SimpleAnnotation(parent, locations, Name):
    return Feature(parent, '', Name, locations)
 
def annotate(parent, start, end, Name):
    annot = parent.addAnnotation(SimpleAnnotation, locations=[(start, end)], Name=Name)

src/p/y/pycogent-HEAD/tests/test_core/test_maps.py   pycogent(Download)
#!/usr/bin/env python
 
import unittest
from cogent.core.location import Map, Span
from cogent.core.annotation import _Annotatable, Feature, _Feature
def SimpleAnnotation(parent, locations, Name):
    return Feature(parent, '', Name, locations)
 
def annotate(parent, start, end, Name):
    annot = parent.addAnnotation(SimpleAnnotation, locations=[(start, end)], Name=Name)

src/p/y/pycogent-HEAD/tests/test_parse/test_genbank.py   pycogent(Download)
    def test_rich_parser(self):
        """correctly constructs +/- strand features"""
        # a custom annotation function
        from cogent.core.annotation import Feature
        def add_annotation(seq, feature, spans):

src/p/y/pycogent-HEAD/tests/test_core/test_annotation.py   pycogent(Download)
 
from cogent import DNA, LoadSeqs
from cogent.core.annotation import Feature, Variable, _Feature
from cogent.core.location import Map, Span, as_map
 

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