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For handling joins etc where a feature location has several parts.

src/b/i/biopython-1.63/Bio/GenBank/__init__.py   biopython(Download)
            #TODO - Remove use of sub_features
            if strand == -1:
                cur_feature.location = SeqFeature.CompoundLocation([f.location for f in sub_features[::-1]],
                                                                   operator=location_line[:i])
            else:
                cur_feature.location = SeqFeature.CompoundLocation([f.location for f in sub_features],
            if strand == -1:
                #Reverse the backwards order used in GenBank files
                cur_feature.location = SeqFeature.CompoundLocation([f.location for f in sub_features[::-1]],
                                                                   operator=location_line[:i])
            else:
                cur_feature.location = SeqFeature.CompoundLocation([f.location for f in sub_features],

src/b/i/biopython-HEAD/Bio/GenBank/__init__.py   biopython(Download)
            #TODO - Remove use of sub_features
            if strand == -1:
                cur_feature.location = SeqFeature.CompoundLocation([f.location for f in sub_features[::-1]],
                                                                   operator=location_line[:i])
            else:
                cur_feature.location = SeqFeature.CompoundLocation([f.location for f in sub_features],
            if strand == -1:
                #Reverse the backwards order used in GenBank files
                cur_feature.location = SeqFeature.CompoundLocation([f.location for f in sub_features[::-1]],
                                                                   operator=location_line[:i])
            else:
                cur_feature.location = SeqFeature.CompoundLocation([f.location for f in sub_features],

src/b/i/biopython-1.63/BioSQL/BioSeq.py   biopython(Download)
                #All forward, or mixed strands
                locs = [f.location for f in sub_features]
            feature.location = SeqFeature.CompoundLocation(locs, seqfeature_type)
            #TODO - See Bug 2677 - we don't yet record location_operator,
            #so for consistency with older versions of Biopython default

src/b/i/biopython-HEAD/BioSQL/BioSeq.py   biopython(Download)
                #All forward, or mixed strands
                locs = [f.location for f in sub_features]
            feature.location = SeqFeature.CompoundLocation(locs, seqfeature_type)
            #TODO - See Bug 2677 - we don't yet record location_operator,
            #so for consistency with older versions of Biopython default

src/p/y/pydna-0.6.1/pydna/utils.py   pydna(Download)
    '''
    from Bio.SeqFeature import SeqFeature
    from Bio.SeqFeature import FeatureLocation, CompoundLocation
    from Bio.SeqRecord  import SeqRecord
    import copy
    def wraparound(feature):
        new_start = length -(shift-feature.location.start)
        new_end   = feature.location.end-shift
 
        c = SeqFeature(CompoundLocation( [FeatureLocation(0, new_end),

src/p/y/pydna-0.6.1/pydna/dsdna.py   pydna(Download)
from Bio.SeqRecord          import SeqRecord
from Bio.SeqFeature         import SeqFeature
from Bio.SeqFeature         import FeatureLocation, CompoundLocation
from Bio.SeqUtils.CheckSum  import seguid
from Bio.GenBank            import RecordParser
                        nps.append(FeatureLocation(part.start-length, part.end-length))
 
                folded_features.append(SeqFeature(CompoundLocation(nps),
                                                  qualifiers = feature.qualifiers,
                                                  type=feature.type))
 
            else:
                folded_features.append(SeqFeature(CompoundLocation([FeatureLocation(feature.location.start, length),

src/p/y/pydna-0.6.1/pydna/amplify.py   pydna(Download)
from Bio.SeqUtils.MeltingTemp       import Tm_staluc
from Bio.SeqFeature                 import SeqFeature
from Bio.SeqFeature                 import CompoundLocation
from Bio.SeqFeature                 import FeatureLocation
from Bio.SeqFeature                 import ExactPosition
                start = len(self.template)-len(fp.footprint)+fp.position
                end = start+len(fp.footprint)-len(self.template)
                sf=SeqFeature(CompoundLocation([FeatureLocation(start,len(self.template)),
                                                FeatureLocation(0, end)]),
                                                type="primer_bind",
                start = rp.position
                end = rp.position+len(rp.footprint)-len(self.template)
                self.template.features.append(SeqFeature(CompoundLocation([FeatureLocation(start,len(self.template)), 
                                                                      FeatureLocation(0,end)]),
                                                    type ="primer_bind",

src/b/i/biopython-1.63/Tests/test_SeqIO_features.py   biopython(Download)
from Bio.Seq import Seq, UnknownSeq, MutableSeq, reverse_complement
from Bio.SeqRecord import SeqRecord
from Bio.SeqFeature import SeqFeature, FeatureLocation, CompoundLocation
from Bio.SeqFeature import ExactPosition, BeforePosition, AfterPosition, \
                           OneOfPosition,  WithinPosition
        #All reverse strand.
        #Historical accident from GenBank parser means sub_features reversed
        c_loc = CompoundLocation([f.location for f in f_list[::-1]])
    else:
        #All forward, or mixed strand
        c_loc = CompoundLocation([f.location for f in f_list])

src/b/i/biopython-HEAD/Tests/test_SeqIO_features.py   biopython(Download)
from Bio.Seq import Seq, UnknownSeq, MutableSeq, reverse_complement
from Bio.SeqRecord import SeqRecord
from Bio.SeqFeature import SeqFeature, FeatureLocation, CompoundLocation
from Bio.SeqFeature import ExactPosition, BeforePosition, AfterPosition, \
                           OneOfPosition,  WithinPosition
        #All reverse strand.
        #Historical accident from GenBank parser means sub_features reversed
        c_loc = CompoundLocation([f.location for f in f_list[::-1]])
    else:
        #All forward, or mixed strand
        c_loc = CompoundLocation([f.location for f in f_list])

src/b/i/biopython-HEAD/Tests/seq_tests_common.py   biopython(Download)
from Bio.SeqUtils.CheckSum import seguid
from Bio.SeqFeature import ExactPosition, UnknownPosition
from Bio.SeqFeature import FeatureLocation, CompoundLocation, SeqFeature
from Bio.SeqRecord import SeqRecord
 

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