Index _ | A | B | C | D | E | F | G | I | K | L | M | N | O | P | Q | R | S | T | U | V | W | X _ __bool__() (pyncbitk.objects.seqinst.DeltaInst method) __buffer__() (pyncbitk.objects.seqdata.IupacAaData method) (pyncbitk.objects.seqdata.IupacNaData method) (pyncbitk.objects.seqdata.Ncbi2NaData method) (pyncbitk.objects.seqdata.Ncbi4NaData method) (pyncbitk.objects.seqdata.Ncbi8NaData method) (pyncbitk.objects.seqdata.NcbiEAaData method) __call__() (pyncbitk.objmgr.BioSeqHandle method) __contains__() (pyncbitk.objmgr.Scope method) (pyncbitk.objtools.DatabaseKeys method) (pyncbitk.objtools.DatabaseValues method) __eq__() (pyncbitk.objects.general.DBTag method) (pyncbitk.objects.seqdata.IupacNaData method) (pyncbitk.objects.seqid.SeqId method) (pyncbitk.serial.Serial method) __ge__() (pyncbitk.objects.general.DBTag method) (pyncbitk.objects.seqdata.IupacNaData method) (pyncbitk.objects.seqid.SeqId method) __getitem__() (pyncbitk.algo.blast.SearchResultsSet method) (pyncbitk.objects.seqalign.SeqAlign method) (pyncbitk.objmgr.Scope method) (pyncbitk.objtools.AlignMap method) (pyncbitk.objtools.DatabaseReader method) __gt__() (pyncbitk.objects.general.DBTag method) (pyncbitk.objects.seqdata.IupacNaData method) (pyncbitk.objects.seqid.SeqId method) __hash__() (pyncbitk.objects.seqid.SeqId method) __init__() (pyncbitk.algo.blast.BlastN method) (pyncbitk.algo.blast.BlastP method) (pyncbitk.algo.blast.BlastX method) (pyncbitk.algo.blast.SearchQuery method) (pyncbitk.algo.blast.SearchQueryVector method) (pyncbitk.algo.blast.TBlastN method) (pyncbitk.objects.general.DBTag method) (pyncbitk.objects.general.ObjectId method) (pyncbitk.objects.seq.BioSeq method) (pyncbitk.objects.seqdata.IupacAaData method) (pyncbitk.objects.seqdata.IupacNaData method) (pyncbitk.objects.seqdata.Ncbi2NaData method) (pyncbitk.objects.seqdata.Ncbi4NaData method) (pyncbitk.objects.seqdata.Ncbi8NaData method) (pyncbitk.objects.seqdata.NcbiEAaData method) (pyncbitk.objects.seqdata.SeqData method) (pyncbitk.objects.seqdesc.NameDesc method) (pyncbitk.objects.seqdesc.RegionDesc method) (pyncbitk.objects.seqdesc.SeqDesc method) (pyncbitk.objects.seqdesc.SeqDescSet method) (pyncbitk.objects.seqdesc.TitleDesc method) (pyncbitk.objects.seqid.LocalId method) (pyncbitk.objects.seqid.TextSeqId method) (pyncbitk.objects.seqinst.ContinuousInst method) (pyncbitk.objects.seqinst.DeltaInst method) (pyncbitk.objects.seqinst.LiteralDelta method) (pyncbitk.objects.seqinst.LocDelta method) (pyncbitk.objects.seqinst.RefInst method) (pyncbitk.objects.seqinst.SeqInst method) (pyncbitk.objects.seqloc.SeqIntervalLoc method) (pyncbitk.objects.seqloc.WholeSeqLoc method) (pyncbitk.objmgr.ObjectManager method) (pyncbitk.objmgr.Scope method) (pyncbitk.objtools.AlignMap method) (pyncbitk.objtools.DatabaseKeys method) (pyncbitk.objtools.DatabaseReader method) (pyncbitk.objtools.DatabaseValues method) (pyncbitk.objtools.DatabaseWriter method) (pyncbitk.objtools.FastaReader method) __iter__() (pyncbitk.objects.seqalign.SeqAlignScore method) (pyncbitk.objects.seqalign.SeqAlignSet method) (pyncbitk.objects.seqdesc.SeqDescSet method) (pyncbitk.objects.seqinst.DeltaInst method) (pyncbitk.objtools.DatabaseKeys method) (pyncbitk.objtools.DatabaseReader method) (pyncbitk.objtools.DatabaseValues method) (pyncbitk.objtools.FastaReader method) __le__() (pyncbitk.objects.general.DBTag method) (pyncbitk.objects.seqdata.IupacNaData method) (pyncbitk.objects.seqid.SeqId method) __len__() (pyncbitk.algo.blast.SearchQueryVector method) (pyncbitk.algo.blast.SearchResultsSet method) (pyncbitk.objects.seqalign.SeqAlign method) (pyncbitk.objects.seqalign.SeqAlignSet method) (pyncbitk.objects.seqdesc.SeqDescSet method) (pyncbitk.objects.seqinst.DeltaInst method) (pyncbitk.objtools.AlignMap method) (pyncbitk.objtools.DatabaseKeys method) (pyncbitk.objtools.DatabaseReader method) (pyncbitk.objtools.DatabaseValues method) __lt__() (pyncbitk.objects.general.DBTag method) (pyncbitk.objects.seqdata.IupacNaData method) (pyncbitk.objects.seqid.SeqId method) __ne__() (pyncbitk.objects.general.DBTag method) (pyncbitk.objects.seqdata.IupacNaData method) (pyncbitk.objects.seqid.SeqId method) __new__() (pyncbitk.algo.blast.Blast class method) (pyncbitk.algo.blast.BlastN class method) (pyncbitk.algo.blast.BlastP class method) (pyncbitk.algo.blast.BlastX class method) (pyncbitk.algo.blast.MappingBlast class method) (pyncbitk.algo.blast.NucleotideBlast class method) (pyncbitk.algo.blast.ProteinBlast class method) (pyncbitk.algo.blast.SearchQuery class method) (pyncbitk.algo.blast.SearchQueryVector class method) (pyncbitk.algo.blast.SearchResults class method) (pyncbitk.algo.blast.SearchResultsSet class method) (pyncbitk.algo.blast.TBlastN class method) (pyncbitk.objects.general.DBTag class method) (pyncbitk.objects.general.ObjectId class method) (pyncbitk.objects.seq.BioSeq class method) (pyncbitk.objects.seqalign.AlignRow class method) (pyncbitk.objects.seqalign.AlignSegments class method) (pyncbitk.objects.seqalign.DenseSegments class method) (pyncbitk.objects.seqalign.DenseSegmentsData class method) (pyncbitk.objects.seqalign.DiagonalSeqAlign class method) (pyncbitk.objects.seqalign.DiscontinuousSeqAlign class method) (pyncbitk.objects.seqalign.GlobalSeqAlign class method) (pyncbitk.objects.seqalign.PartialSeqAlign class method) (pyncbitk.objects.seqalign.SeqAlign class method) (pyncbitk.objects.seqalign.SeqAlignScore class method) (pyncbitk.objects.seqalign.SeqAlignSet class method) (pyncbitk.objects.seqdata.GapData class method) (pyncbitk.objects.seqdata.IupacAaData class method) (pyncbitk.objects.seqdata.IupacNaData class method) (pyncbitk.objects.seqdata.Ncbi2NaData class method) (pyncbitk.objects.seqdata.Ncbi4NaData class method) (pyncbitk.objects.seqdata.Ncbi8AaData class method) (pyncbitk.objects.seqdata.Ncbi8NaData class method) (pyncbitk.objects.seqdata.NcbiEAaData class method) (pyncbitk.objects.seqdata.NcbiPAaData class method) (pyncbitk.objects.seqdata.NcbiPNaData class method) (pyncbitk.objects.seqdata.NcbiStdAa class method) (pyncbitk.objects.seqdata.SeqAaData class method) (pyncbitk.objects.seqdata.SeqData class method) (pyncbitk.objects.seqdata.SeqNaData class method) (pyncbitk.objects.seqdesc.NameDesc class method) (pyncbitk.objects.seqdesc.RegionDesc class method) (pyncbitk.objects.seqdesc.SeqDesc class method) (pyncbitk.objects.seqdesc.SeqDescSet class method) (pyncbitk.objects.seqdesc.TitleDesc class method) (pyncbitk.objects.seqid.GenBankId class method) (pyncbitk.objects.seqid.GeneralId class method) (pyncbitk.objects.seqid.LocalId class method) (pyncbitk.objects.seqid.OtherId class method) (pyncbitk.objects.seqid.ProteinDataBankId class method) (pyncbitk.objects.seqid.RefSeqId class method) (pyncbitk.objects.seqid.SeqId class method) (pyncbitk.objects.seqid.TextSeqId class method) (pyncbitk.objects.seqinst.ConsensusInst class method) (pyncbitk.objects.seqinst.ConstructedInst class method) (pyncbitk.objects.seqinst.ContinuousInst class method) (pyncbitk.objects.seqinst.Delta class method) (pyncbitk.objects.seqinst.DeltaInst class method) (pyncbitk.objects.seqinst.LiteralDelta class method) (pyncbitk.objects.seqinst.LocDelta class method) (pyncbitk.objects.seqinst.MapInst class method) (pyncbitk.objects.seqinst.RefInst class method) (pyncbitk.objects.seqinst.SegmentedInst class method) (pyncbitk.objects.seqinst.SeqInst class method) (pyncbitk.objects.seqinst.VirtualInst class method) (pyncbitk.objects.seqloc.BondLoc class method) (pyncbitk.objects.seqloc.EmptySeqLoc class method) (pyncbitk.objects.seqloc.EquivalentLoc class method) (pyncbitk.objects.seqloc.FeatureLoc class method) (pyncbitk.objects.seqloc.MixLoc class method) (pyncbitk.objects.seqloc.NullLoc class method) (pyncbitk.objects.seqloc.PackedPointsLoc class method) (pyncbitk.objects.seqloc.PackedSeqLoc class method) (pyncbitk.objects.seqloc.PointLoc class method) (pyncbitk.objects.seqloc.SeqIntervalLoc class method) (pyncbitk.objects.seqloc.SeqLoc class method) (pyncbitk.objects.seqloc.WholeSeqLoc class method) (pyncbitk.objmgr.BioSeqHandle class method) (pyncbitk.objmgr.ObjectManager class method) (pyncbitk.objmgr.Scope class method) (pyncbitk.objtools.AlignMap class method) (pyncbitk.objtools.AlignMapRow class method) (pyncbitk.objtools.DatabaseKeys class method) (pyncbitk.objtools.DatabaseReader class method) (pyncbitk.objtools.DatabaseValues class method) (pyncbitk.objtools.DatabaseWriter class method) (pyncbitk.objtools.FastaReader class method) __reduce__() (pyncbitk.algo.blast.Blast method) (pyncbitk.algo.blast.BlastN method) (pyncbitk.algo.blast.BlastP method) (pyncbitk.algo.blast.BlastX method) (pyncbitk.algo.blast.MappingBlast method) (pyncbitk.algo.blast.NucleotideBlast method) (pyncbitk.algo.blast.ProteinBlast method) (pyncbitk.algo.blast.SearchQuery method) (pyncbitk.algo.blast.SearchQueryVector method) (pyncbitk.algo.blast.SearchResults method) (pyncbitk.algo.blast.SearchResultsSet method) (pyncbitk.algo.blast.TBlastN method) (pyncbitk.objects.general.DBTag method) (pyncbitk.objects.general.ObjectId method) (pyncbitk.objects.seq.BioSeq method) (pyncbitk.objects.seqalign.AlignRow method) (pyncbitk.objects.seqalign.AlignSegments method) (pyncbitk.objects.seqalign.DenseSegments method) (pyncbitk.objects.seqalign.DenseSegmentsData method) (pyncbitk.objects.seqalign.DiagonalSeqAlign method) (pyncbitk.objects.seqalign.DiscontinuousSeqAlign method) (pyncbitk.objects.seqalign.GlobalSeqAlign method) (pyncbitk.objects.seqalign.PartialSeqAlign method) (pyncbitk.objects.seqalign.SeqAlign method) (pyncbitk.objects.seqalign.SeqAlignScore method) (pyncbitk.objects.seqalign.SeqAlignSet method) (pyncbitk.objects.seqdata.GapData method) (pyncbitk.objects.seqdata.Ncbi8AaData method) (pyncbitk.objects.seqdata.NcbiPAaData method) (pyncbitk.objects.seqdata.NcbiPNaData method) (pyncbitk.objects.seqdata.NcbiStdAa method) (pyncbitk.objects.seqdata.SeqAaData method) (pyncbitk.objects.seqdata.SeqData method) (pyncbitk.objects.seqdata.SeqNaData method) (pyncbitk.objects.seqdesc.NameDesc method) (pyncbitk.objects.seqdesc.RegionDesc method) (pyncbitk.objects.seqdesc.SeqDesc method) (pyncbitk.objects.seqdesc.SeqDescSet method) (pyncbitk.objects.seqdesc.TitleDesc method) (pyncbitk.objects.seqid.GenBankId method) (pyncbitk.objects.seqid.GeneralId method) (pyncbitk.objects.seqid.LocalId method) (pyncbitk.objects.seqid.OtherId method) (pyncbitk.objects.seqid.ProteinDataBankId method) (pyncbitk.objects.seqid.RefSeqId method) (pyncbitk.objects.seqid.SeqId method) (pyncbitk.objects.seqid.TextSeqId method) (pyncbitk.objects.seqinst.ConsensusInst method) (pyncbitk.objects.seqinst.ConstructedInst method) (pyncbitk.objects.seqinst.ContinuousInst method) (pyncbitk.objects.seqinst.Delta method) (pyncbitk.objects.seqinst.DeltaInst method) (pyncbitk.objects.seqinst.LiteralDelta method) (pyncbitk.objects.seqinst.LocDelta method) (pyncbitk.objects.seqinst.MapInst method) (pyncbitk.objects.seqinst.RefInst method) (pyncbitk.objects.seqinst.SegmentedInst method) (pyncbitk.objects.seqinst.SeqInst method) (pyncbitk.objects.seqinst.VirtualInst method) (pyncbitk.objects.seqloc.BondLoc method) (pyncbitk.objects.seqloc.EmptySeqLoc method) (pyncbitk.objects.seqloc.EquivalentLoc method) (pyncbitk.objects.seqloc.FeatureLoc method) (pyncbitk.objects.seqloc.MixLoc method) (pyncbitk.objects.seqloc.NullLoc method) (pyncbitk.objects.seqloc.PackedPointsLoc method) (pyncbitk.objects.seqloc.PackedSeqLoc method) (pyncbitk.objects.seqloc.PointLoc method) (pyncbitk.objects.seqloc.SeqIntervalLoc method) (pyncbitk.objects.seqloc.SeqLoc method) (pyncbitk.objects.seqloc.WholeSeqLoc method) (pyncbitk.objmgr.BioSeqHandle method) (pyncbitk.objmgr.ObjectManager method) (pyncbitk.objmgr.Scope method) (pyncbitk.objtools.AlignMap method) (pyncbitk.objtools.AlignMapRow method) (pyncbitk.objtools.DatabaseKeys method) (pyncbitk.objtools.DatabaseReader method) (pyncbitk.objtools.DatabaseValues method) (pyncbitk.objtools.DatabaseWriter method) (pyncbitk.objtools.FastaReader method) __reduce_ex__() (pyncbitk.objects.seqdata.IupacAaData method) (pyncbitk.objects.seqdata.IupacNaData method) (pyncbitk.objects.seqdata.Ncbi2NaData method) (pyncbitk.objects.seqdata.Ncbi4NaData method) (pyncbitk.objects.seqdata.Ncbi8NaData method) (pyncbitk.objects.seqdata.NcbiEAaData method) __repr__() (pyncbitk.algo.blast.Blast method) (pyncbitk.objects.general.DBTag method) (pyncbitk.objects.general.ObjectId method) (pyncbitk.objects.seq.BioSeq method) (pyncbitk.objects.seqalign.SeqAlignScore method) (pyncbitk.objects.seqdata.IupacAaData method) (pyncbitk.objects.seqdata.IupacNaData method) (pyncbitk.objects.seqdata.Ncbi2NaData method) (pyncbitk.objects.seqdata.Ncbi4NaData method) (pyncbitk.objects.seqdata.Ncbi8NaData method) (pyncbitk.objects.seqdata.NcbiEAaData method) (pyncbitk.objects.seqdesc.NameDesc method) (pyncbitk.objects.seqdesc.RegionDesc method) (pyncbitk.objects.seqdesc.TitleDesc method) (pyncbitk.objects.seqid.GenBankId method) (pyncbitk.objects.seqid.GeneralId method) (pyncbitk.objects.seqid.LocalId method) (pyncbitk.objects.seqid.OtherId method) (pyncbitk.objects.seqid.TextSeqId method) (pyncbitk.objects.seqinst.ContinuousInst method) (pyncbitk.objects.seqinst.DeltaInst method) (pyncbitk.objects.seqinst.LiteralDelta method) (pyncbitk.objects.seqinst.LocDelta method) (pyncbitk.objects.seqinst.RefInst method) (pyncbitk.objects.seqinst.SeqInst method) (pyncbitk.objects.seqloc.SeqIntervalLoc method) (pyncbitk.objects.seqloc.WholeSeqLoc method) __str__() (pyncbitk.objects.general.ObjectId method) (pyncbitk.objects.seqdesc.NameDesc method) (pyncbitk.objects.seqdesc.RegionDesc method) (pyncbitk.objects.seqdesc.TitleDesc method) (pyncbitk.objects.seqid.LocalId method) A accession (pyncbitk.objects.seqid.TextSeqId attribute) AlignMap (class in pyncbitk.objtools) AlignMapRow (class in pyncbitk.objtools) alignment_length (pyncbitk.objects.seqalign.SeqAlign attribute) AlignRow (class in pyncbitk.objects.seqalign) AlignSegments (class in pyncbitk.objects.seqalign) append() (pyncbitk.objtools.DatabaseWriter method) B BioSeq (class in pyncbitk.objects.seq) BioSeqHandle (class in pyncbitk.objmgr) bitscore (pyncbitk.objects.seqalign.SeqAlign attribute) Blast (class in pyncbitk.algo.blast) BlastN (class in pyncbitk.algo.blast) BlastP (class in pyncbitk.algo.blast) BlastX (class in pyncbitk.algo.blast) BondLoc (class in pyncbitk.objects.seqloc) C close() (pyncbitk.objmgr.Scope method) (pyncbitk.objtools.DatabaseWriter method) ConsensusInst (class in pyncbitk.objects.seqinst) ConstructedInst (class in pyncbitk.objects.seqinst) ContinuousInst (class in pyncbitk.objects.seqinst) copy() (pyncbitk.objects.seqdata.SeqData method) coverage_hsp (pyncbitk.algo.blast.Blast attribute) culling_limit (pyncbitk.algo.blast.Blast attribute) D data (pyncbitk.objects.seqdata.IupacAaData attribute) (pyncbitk.objects.seqdata.IupacNaData attribute) (pyncbitk.objects.seqdata.Ncbi2NaData attribute) (pyncbitk.objects.seqdata.Ncbi4NaData attribute) (pyncbitk.objects.seqdata.Ncbi8NaData attribute) (pyncbitk.objects.seqdata.NcbiEAaData attribute) (pyncbitk.objects.seqinst.ContinuousInst attribute) (pyncbitk.objects.seqinst.LiteralDelta attribute) database_genetic_code (pyncbitk.algo.blast.TBlastN attribute) database_size (pyncbitk.algo.blast.Blast attribute) DatabaseKeys (class in pyncbitk.objtools) DatabaseReader (class in pyncbitk.objtools) DatabaseValues (class in pyncbitk.objtools) DatabaseWriter (class in pyncbitk.objtools) db (pyncbitk.objects.general.DBTag attribute) db_tag (pyncbitk.objects.seqid.GeneralId attribute) DBTag (class in pyncbitk.objects.general) decode() (pyncbitk.objects.seqdata.IupacAaData method) (pyncbitk.objects.seqdata.IupacNaData method) (pyncbitk.objects.seqdata.NcbiEAaData method) (pyncbitk.objects.seqdata.SeqAaData method) (pyncbitk.objects.seqdata.SeqNaData method) Delta (class in pyncbitk.objects.seqinst) DeltaInst (class in pyncbitk.objects.seqinst) DenseSegments (class in pyncbitk.objects.seqalign) DenseSegmentsData (class in pyncbitk.objects.seqalign) descriptions (pyncbitk.objects.seq.BioSeq attribute) (pyncbitk.objmgr.BioSeqHandle attribute) DiagonalSeqAlign (class in pyncbitk.objects.seqalign) DiscontinuousSeqAlign (class in pyncbitk.objects.seqalign) dumps() (pyncbitk.serial.Serial method) dust_filtering (pyncbitk.algo.blast.BlastN attribute) E EmptySeqLoc (class in pyncbitk.objects.seqloc) encode() (pyncbitk.objects.seqdata.IupacAaData class method) (pyncbitk.objects.seqdata.IupacNaData class method) (pyncbitk.objects.seqdata.NcbiEAaData class method) (pyncbitk.objects.seqdata.SeqAaData class method) (pyncbitk.objects.seqdata.SeqNaData class method) EquivalentLoc (class in pyncbitk.objects.seqloc) evalue (pyncbitk.algo.blast.Blast attribute) (pyncbitk.objects.seqalign.SeqAlign attribute) F FastaReader (class in pyncbitk.objtools) FeatureLoc (class in pyncbitk.objects.seqloc) files (pyncbitk.objtools.DatabaseWriter attribute) G GapData (class in pyncbitk.objects.seqdata) gapped (pyncbitk.algo.blast.Blast attribute) GenBankId (class in pyncbitk.objects.seqid) GeneralId (class in pyncbitk.objects.seqid) GlobalSeqAlign (class in pyncbitk.objects.seqalign) I id (pyncbitk.objects.seq.BioSeq attribute) (pyncbitk.objects.seqid.GenBankId attribute) (pyncbitk.objects.seqid.OtherId attribute) (pyncbitk.objmgr.BioSeqHandle attribute) ids (pyncbitk.objects.seq.BioSeq attribute) (pyncbitk.objects.seqalign.DenseSegmentsData attribute) (pyncbitk.objmgr.BioSeqHandle attribute) instance (pyncbitk.objects.seq.BioSeq attribute) (pyncbitk.objmgr.BioSeqHandle attribute) IupacAaData (class in pyncbitk.objects.seqdata) IupacNaData (class in pyncbitk.objects.seqdata) K keys() (pyncbitk.objtools.DatabaseReader method) L length (pyncbitk.objects.seqdata.IupacAaData attribute) (pyncbitk.objects.seqdata.IupacNaData attribute) (pyncbitk.objects.seqdata.NcbiEAaData attribute) (pyncbitk.objects.seqinst.LiteralDelta attribute) (pyncbitk.objects.seqinst.SeqInst attribute) (pyncbitk.objmgr.BioSeqHandle attribute) lengths (pyncbitk.objects.seqalign.DenseSegmentsData attribute) LiteralDelta (class in pyncbitk.objects.seqinst) LocalId (class in pyncbitk.objects.seqid) LocDelta (class in pyncbitk.objects.seqinst) M MapInst (class in pyncbitk.objects.seqinst) MappingBlast (class in pyncbitk.algo.blast) master_coverage() (pyncbitk.objects.seqalign.SeqAlignSet method) max_intron_length (pyncbitk.algo.blast.BlastX attribute) (pyncbitk.algo.blast.TBlastN attribute) max_target_sequences (pyncbitk.algo.blast.Blast attribute) MixLoc (class in pyncbitk.objects.seqloc) module pyncbitk pyncbitk.algo pyncbitk.objects pyncbitk.objects.general pyncbitk.objects.seq pyncbitk.objects.seqalign pyncbitk.objects.seqdata pyncbitk.objects.seqdesc pyncbitk.objects.seqid pyncbitk.objects.seqinst pyncbitk.objects.seqloc pyncbitk.objmgr pyncbitk.objtools pyncbitk.serial molecule (pyncbitk.objects.seqinst.SeqInst attribute) N name (pyncbitk.objects.seqid.TextSeqId attribute) NameDesc (class in pyncbitk.objects.seqdesc) Ncbi2NaData (class in pyncbitk.objects.seqdata) Ncbi4NaData (class in pyncbitk.objects.seqdata) Ncbi8AaData (class in pyncbitk.objects.seqdata) Ncbi8NaData (class in pyncbitk.objects.seqdata) NcbiEAaData (class in pyncbitk.objects.seqdata) NcbiPAaData (class in pyncbitk.objects.seqdata) NcbiPNaData (class in pyncbitk.objects.seqdata) NcbiStdAa (class in pyncbitk.objects.seqdata) NucleotideBlast (class in pyncbitk.algo.blast) NullLoc (class in pyncbitk.objects.seqloc) O object_id (pyncbitk.objects.seqid.LocalId attribute) ObjectId (class in pyncbitk.objects.general) ObjectManager (class in pyncbitk.objmgr) off_diagonal_range (pyncbitk.algo.blast.Blast attribute) OtherId (class in pyncbitk.objects.seqid) P PackedPointsLoc (class in pyncbitk.objects.seqloc) PackedSeqLoc (class in pyncbitk.objects.seqloc) parse() (pyncbitk.objects.seqid.SeqId static method) PartialSeqAlign (class in pyncbitk.objects.seqalign) penalty (pyncbitk.algo.blast.BlastN attribute) percent_coverage (pyncbitk.objects.seqalign.SeqAlign attribute) percent_identity (pyncbitk.algo.blast.Blast attribute) (pyncbitk.objects.seqalign.SeqAlign attribute) PointLoc (class in pyncbitk.objects.seqloc) program (pyncbitk.algo.blast.Blast attribute) ProteinBlast (class in pyncbitk.algo.blast) ProteinDataBankId (class in pyncbitk.objects.seqid) pyncbitk module pyncbitk.algo module pyncbitk.objects module pyncbitk.objects.general module pyncbitk.objects.seq module pyncbitk.objects.seqalign module pyncbitk.objects.seqdata module pyncbitk.objects.seqdesc module pyncbitk.objects.seqid module pyncbitk.objects.seqinst module pyncbitk.objects.seqloc module pyncbitk.objmgr module pyncbitk.objtools module pyncbitk.serial module Q query_genetic_code (pyncbitk.algo.blast.BlastX attribute) R read() (pyncbitk.objtools.FastaReader method) RefInst (class in pyncbitk.objects.seqinst) RefSeqId (class in pyncbitk.objects.seqid) RegionDesc (class in pyncbitk.objects.seqdesc) release (pyncbitk.objects.seqid.TextSeqId attribute) reward (pyncbitk.algo.blast.BlastN attribute) run (pyncbitk.algo.blast.Blast attribute) S Scope (class in pyncbitk.objmgr) scope() (pyncbitk.objmgr.ObjectManager method) search_space (pyncbitk.algo.blast.Blast attribute) SearchQuery (class in pyncbitk.algo.blast) SearchQueryVector (class in pyncbitk.algo.blast) SearchResults (class in pyncbitk.algo.blast) SearchResultsSet (class in pyncbitk.algo.blast) SegmentedInst (class in pyncbitk.objects.seqinst) SeqAaData (class in pyncbitk.objects.seqdata) SeqAlign (class in pyncbitk.objects.seqalign) SeqAlignScore (class in pyncbitk.objects.seqalign) SeqAlignSet (class in pyncbitk.objects.seqalign) SeqData (class in pyncbitk.objects.seqdata) SeqDesc (class in pyncbitk.objects.seqdesc) SeqDescSet (class in pyncbitk.objects.seqdesc) SeqId (class in pyncbitk.objects.seqid) SeqInst (class in pyncbitk.objects.seqinst) SeqIntervalLoc (class in pyncbitk.objects.seqloc) SeqLoc (class in pyncbitk.objects.seqloc) seqloc (pyncbitk.objects.seqinst.LocDelta attribute) (pyncbitk.objects.seqinst.RefInst attribute) SeqNaData (class in pyncbitk.objects.seqdata) sequence_id (pyncbitk.objects.seqloc.SeqIntervalLoc attribute) (pyncbitk.objects.seqloc.WholeSeqLoc attribute) Serial (class in pyncbitk.serial) start (pyncbitk.objects.seqloc.SeqIntervalLoc attribute) starts (pyncbitk.objects.seqalign.DenseSegmentsData attribute) stop (pyncbitk.objects.seqloc.SeqIntervalLoc attribute) strandedness (pyncbitk.objects.seqinst.SeqInst attribute) strands (pyncbitk.objects.seqalign.DenseSegmentsData attribute) T tag (pyncbitk.objects.general.DBTag attribute) TBlastN (class in pyncbitk.algo.blast) TextSeqId (class in pyncbitk.objects.seqid) TitleDesc (class in pyncbitk.objects.seqdesc) to_continuous() (pyncbitk.objects.seqinst.DeltaInst method) topology (pyncbitk.objects.seqinst.SeqInst attribute) U url() (pyncbitk.objects.general.DBTag method) V value (pyncbitk.objects.general.ObjectId attribute) values() (pyncbitk.objtools.DatabaseReader method) version (pyncbitk.objects.seqid.TextSeqId attribute) (pyncbitk.objtools.DatabaseReader attribute) VirtualInst (class in pyncbitk.objects.seqinst) volumes (pyncbitk.objtools.DatabaseWriter attribute) W WholeSeqLoc (class in pyncbitk.objects.seqloc) window_size (pyncbitk.algo.blast.Blast attribute) word_size (pyncbitk.algo.blast.BlastP attribute) word_threshold (pyncbitk.algo.blast.BlastP attribute) X xdrop_gap (pyncbitk.algo.blast.Blast attribute) xdrop_gap_final (pyncbitk.algo.blast.Blast attribute)