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src/b/i/biopython-1.63/Bio/GenBank/__init__.py   biopython(Download)
        else:
            default = e
        return SeqFeature.WithinPosition(default, left=s, right=e)
    elif _re_oneof_position.match(pos_str):
        assert pos_str.startswith("one-of(")

src/b/i/biopython-HEAD/Bio/GenBank/__init__.py   biopython(Download)
        else:
            default = e
        return SeqFeature.WithinPosition(default, left=s, right=e)
    elif _re_oneof_position.match(pos_str):
        assert pos_str.startswith("one-of(")

src/b/i/biopython-1.63/Tests/test_SeqIO_features.py   biopython(Download)
from Bio.SeqRecord import SeqRecord
from Bio.SeqFeature import SeqFeature, FeatureLocation, CompoundLocation
from Bio.SeqFeature import ExactPosition, BeforePosition, AfterPosition, \
                           OneOfPosition,  WithinPosition
 
                        strand=+1)
        f2 = SeqFeature(FeatureLocation(125, 140), strand=+1)
        f3 = SeqFeature(FeatureLocation(145, WithinPosition(160, left=150, right=160)), strand=+1)
        f = make_join_feature([f1, f2, f3], "CDS")
        self.assertEqual(_insdc_feature_location_string(f, 500),
 
        f1 = SeqFeature(FeatureLocation(BeforePosition(210), 220), strand=-1)
        f2 = SeqFeature(FeatureLocation(225, WithinPosition(244, left=240, right=244)), strand=-1)
        f = make_join_feature([f1, f2], "gene")
        self.assertEqual(_insdc_feature_location_string(f, 500),
                                                                ExactPosition(337)])),
                        strand=-1)
        f3 = SeqFeature(FeatureLocation(345, WithinPosition(355, left=350, right=355)), strand=-1)
        f = make_join_feature([f1, f2, f3], "CDS")
        self.assertEqual(_insdc_feature_location_string(f, 500),
    def test_within(self):
        """Features: write/read simple within locations."""
        s = "N" * 100
        f = SeqFeature(FeatureLocation(WithinPosition(2, left=2, right=8), 10),
                       strand=+1, type="CDS")

src/b/i/biopython-HEAD/Tests/test_SeqIO_features.py   biopython(Download)
from Bio.SeqRecord import SeqRecord
from Bio.SeqFeature import SeqFeature, FeatureLocation, CompoundLocation
from Bio.SeqFeature import ExactPosition, BeforePosition, AfterPosition, \
                           OneOfPosition,  WithinPosition
 
                        strand=+1)
        f2 = SeqFeature(FeatureLocation(125, 140), strand=+1)
        f3 = SeqFeature(FeatureLocation(145, WithinPosition(160, left=150, right=160)), strand=+1)
        f = make_join_feature([f1, f2, f3], "CDS")
        self.assertEqual(_insdc_feature_location_string(f, 500),
 
        f1 = SeqFeature(FeatureLocation(BeforePosition(210), 220), strand=-1)
        f2 = SeqFeature(FeatureLocation(225, WithinPosition(244, left=240, right=244)), strand=-1)
        f = make_join_feature([f1, f2], "gene")
        self.assertEqual(_insdc_feature_location_string(f, 500),
                                                                ExactPosition(337)])),
                        strand=-1)
        f3 = SeqFeature(FeatureLocation(345, WithinPosition(355, left=350, right=355)), strand=-1)
        f = make_join_feature([f1, f2, f3], "CDS")
        self.assertEqual(_insdc_feature_location_string(f, 500),
    def test_within(self):
        """Features: write/read simple within locations."""
        s = "N" * 100
        f = SeqFeature(FeatureLocation(WithinPosition(2, left=2, right=8), 10),
                       strand=+1, type="CDS")

src/b/i/biopython-1.63/Tests/test_SeqRecord.py   biopython(Download)
from Bio.SeqRecord import SeqRecord
from Bio.SeqFeature import SeqFeature, FeatureLocation, ExactPosition
from Bio.SeqFeature import WithinPosition, BeforePosition, AfterPosition, OneOfPosition
 
 
    def setUp(self) :
        f0 = SeqFeature(FeatureLocation(0, 26), type="source",
                        qualifiers={"mol_type":["fake protein"]})
        f1 = SeqFeature(FeatureLocation(0, ExactPosition(10)))
        f2 = SeqFeature(FeatureLocation(WithinPosition(12, left=12, right=15), BeforePosition(22)))

src/b/i/biopython-HEAD/Tests/test_SeqRecord.py   biopython(Download)
from Bio.SeqRecord import SeqRecord
from Bio.SeqFeature import SeqFeature, FeatureLocation, ExactPosition
from Bio.SeqFeature import WithinPosition, BeforePosition, AfterPosition, OneOfPosition
 
 
    def setUp(self) :
        f0 = SeqFeature(FeatureLocation(0, 26), type="source",
                        qualifiers={"mol_type":["fake protein"]})
        f1 = SeqFeature(FeatureLocation(0, ExactPosition(10)))
        f2 = SeqFeature(FeatureLocation(WithinPosition(12, left=12, right=15), BeforePosition(22)))

src/b/i/biopython-1.63/Tests/test_Location.py   biopython(Download)
# check the positions alone
exact_pos = SeqFeature.ExactPosition(5)
within_pos_s = SeqFeature.WithinPosition(10, left=10, right=13)
within_pos_e = SeqFeature.WithinPosition(13, left=10, right=13)
between_pos_e = SeqFeature.BetweenPosition(24, left=20, right=24)

src/b/i/biopython-HEAD/Tests/test_Location.py   biopython(Download)
# check the positions alone
exact_pos = SeqFeature.ExactPosition(5)
within_pos_s = SeqFeature.WithinPosition(10, left=10, right=13)
within_pos_e = SeqFeature.WithinPosition(13, left=10, right=13)
between_pos_e = SeqFeature.BetweenPosition(24, left=20, right=24)