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Represent a Sequence Feature on an object.

Attributes:
o location - the location of the feature on the sequence (FeatureLocation)
o type - the specified type of the feature (ie. CDS, exon, repeat...)
o location_operator - a string specifying how this SeqFeature may
be related to others. For example, in the example GenBank feature
shown below, the location_operator would be "join". This is a proxy
for feature.location.operator and only applies to compound locations.
o strand - A value specifying on which strand (of a DNA sequence, for(more...)

src/p/y/python-dna-0.1.2/pydna/assembly.py   python-dna(Download)
#from find_sub_strings         import common_sub_strings
from Bio.Alphabet.IUPAC      import ambiguous_dna
from Bio.SeqFeature          import SeqFeature, FeatureLocation, ExactPosition
from pydna._simple_paths7    import all_circular_paths_edges
from pydna._simple_paths8    import all_simple_paths_edges
                continue
            if end > length:
                a = SeqFeature(FeatureLocation(feature.location.start, length),
                               type=feature.type,
                               location_operator=feature.location_operator,
                               strand=feature.strand,
                               id=feature.id,
                               qualifiers=feature.qualifiers,
                               sub_features=None)
                b = SeqFeature(FeatureLocation(0, feature.location.end-length),
                               qualifiers=feature.qualifiers,
                               sub_features=None)
                newf = SeqFeature(FeatureLocation(a.location.start, b.location.end),
                               type=feature.type,
                               location_operator="join",
                               sub_features=[a,b])
            else:
                newf = SeqFeature(FeatureLocation(begin, end),
                                  type=feature.type,
                                  location_operator=feature.location_operator,

src/p/y/pydna-0.6.1/pydna/utils.py   pydna(Download)
from Bio.SeqUtils.CheckSum  import seguid
from itertools import tee, izip
from Bio.SeqFeature import SeqFeature
from Bio.SeqFeature import FeatureLocation
 
    pydna.dsdna.Dseqrecord.shifted
    '''
    from Bio.SeqFeature import SeqFeature
    from Bio.SeqFeature import FeatureLocation, CompoundLocation
    from Bio.SeqRecord  import SeqRecord
    def wraparound(feature):
        new_start = length -(shift-feature.location.start)
        new_end   = feature.location.end-shift
 
        c = SeqFeature(CompoundLocation( [FeatureLocation(0, new_end),
        for sf in feature.sub_features:
            if feature.location.end<shift:
                sub_features.append(SeqFeature(FeatureLocation(length-feature.location.start,
                                                               length-feature.location.end),
                                    type=feature.type,
                                    sub_features=None))
            elif feature.location.start>shift:
                sub_features.append(SeqFeature(FeatureLocation(feature.location.start-shift,
                                                               feature.location.end-shift),
                                    type=feature.type,

src/p/y/python-dna-0.1.2/pydna/utils.py   python-dna(Download)
'''
 
from Bio.SeqFeature import SeqFeature
from Bio.SeqFeature import FeatureLocation
 
 
    '''
    from Bio.SeqFeature import SeqFeature
    from Bio.SeqFeature import FeatureLocation
    from Bio.SeqRecord  import SeqRecord
    def wraparound(feature):
        new_start = length -(shift-feature.location.start)
        new_end   = feature.location.end-shift
        a = SeqFeature(FeatureLocation(0, new_end),
                       type=feature.type,
                       qualifiers=feature.qualifiers,
                       sub_features=None)
        b = SeqFeature(FeatureLocation(new_start, length),
                       type=feature.type,
                       location_operator=feature.location_operator,
                       strand=feature.strand,
                       id=feature.id,
                       qualifiers=feature.qualifiers,
                       sub_features=None)
        c = SeqFeature(FeatureLocation(new_start, new_end),

src/p/y/python-dna-0.1.2/pydna/dsdna.py   python-dna(Download)
from Bio.Data.IUPACData     import ambiguous_dna_complement as amb_compl
from Bio.SeqRecord          import SeqRecord
from Bio.SeqFeature         import SeqFeature
from Bio.SeqFeature         import FeatureLocation
from Bio.SeqUtils.CheckSum  import seguid
            subfl2 =  FeatureLocation(0, len(feature)-len(subfl1))
 
            sub1 = SeqFeature(subfl1,
                              type=feature.type,
                              location_operator=feature.location_operator,
                              strand=feature.strand,
                              id=feature.id,
                              qualifiers=feature.qualifiers,
                              sub_features=None)
            sub2 = SeqFeature(subfl2,
                              qualifiers=feature.qualifiers,
                              sub_features=None)
            pf =    SeqFeature(FeatureLocation(subfl1.start, subfl2.end),
                              type=feature.type,
                              location_operator="join",

src/p/y/python-dna-0.1.2/pydna/amplify.py   python-dna(Download)
from Bio.SeqUtils                   import GC
from Bio.SeqUtils.MeltingTemp       import Tm_staluc
from Bio.SeqFeature                 import SeqFeature
from Bio.SeqFeature                 import FeatureLocation
from Bio.SeqFeature                 import ExactPosition
                                                  self.reverse_primer.primer.name)
 
        self.product.features.append(SeqFeature(FeatureLocation(0,len(self.forward_primer.primer)),
                                       type ="primer_bind",strand = 1,
                                       qualifiers = {"note":self.forward_primer.primer.name}))
        self.product.features.append(SeqFeature(FeatureLocation(length - len(self.reverse_primer.primer),length),
                start = primer.pos-len(primer.footprint)
                end = primer.pos
                template.features.append(SeqFeature(FeatureLocation(start,end+1),type ="primer_bind",strand = 1, qualifiers = {"note":fp.name,"ApEinfo_fwdcolor":"green","ApEinfo_revcolor":"red"}))
            else:
                start = len(template)-len(primer.footprint)+primer.pos
                end = start+len(primer.footprint)-len(template)
 
                suba = SeqFeature( FeatureLocation(start,len(template)),

src/p/y/pydna-0.6.1/pydna/amplify.py   pydna(Download)
from Bio.SeqUtils                   import GC
from Bio.SeqUtils.MeltingTemp       import Tm_staluc
from Bio.SeqFeature                 import SeqFeature
from Bio.SeqFeature                 import CompoundLocation
from Bio.SeqFeature                 import FeatureLocation
                start = fp.position-len(fp.footprint)
                end   = fp.position
                self.template.features.append(SeqFeature(FeatureLocation(start, end),
                                                    type ="primer_bind",
                                                    strand = 1, 
                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)
                self.template.features.append(SeqFeature(FeatureLocation(start,end),
                                                    type ="primer_bind",
                                                    strand = -1, 
                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/Bio/GenBank/__init__.py   biopython(Download)
    def feature_key(self, content):
        # start a new feature
        self._cur_feature = SeqFeature.SeqFeature()
        self._cur_feature.type = content
        self.data.features.append(self._cur_feature)
            for part in location_line[i+1:-1].split(","):
                s, e = part.split("..")
                f = SeqFeature.SeqFeature(SeqFeature.FeatureLocation(int(s)-1,
                                                                     int(e),
                                                                     strand),
                    print(part)
                    raise err
                f = SeqFeature.SeqFeature(location=loc, ref=ref,
                        location_operator=cur_feature.location_operator,
                        type=cur_feature.type)

src/b/i/biopython-HEAD/Bio/GenBank/__init__.py   biopython(Download)
    def feature_key(self, content):
        # start a new feature
        self._cur_feature = SeqFeature.SeqFeature()
        self._cur_feature.type = content
        self.data.features.append(self._cur_feature)
            for part in location_line[i+1:-1].split(","):
                s, e = part.split("..")
                f = SeqFeature.SeqFeature(SeqFeature.FeatureLocation(int(s)-1,
                                                                     int(e),
                                                                     strand),
                    print(part)
                    raise err
                f = SeqFeature.SeqFeature(location=loc, ref=ref,
                        location_operator=cur_feature.location_operator,
                        type=cur_feature.type)

src/b/i/biopython-1.63/Bio/SeqIO/SwissIO.py   biopython(Download)
    if not ft_id:
        ft_id = "<unknown id>"  # The default in SeqFeature object
    return SeqFeature.SeqFeature(loc, type=name, id=ft_id,
                                 qualifiers={"description": description})
 

src/b/i/biopython-HEAD/Bio/SeqIO/SwissIO.py   biopython(Download)
    if not ft_id:
        ft_id = "<unknown id>"  # The default in SeqFeature object
    return SeqFeature.SeqFeature(loc, type=name, id=ft_id,
                                 qualifiers={"description": description})
 

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