Index _ | A | B | C | D | E | F | G | H | I | L | M | N | O | P | R | S | T | U | W _ _BioBasketStr (class in sugar.core.seq) _BioSeqStr (class in sugar.core.seq) _read_motifs_meme_txt() (in module sugar._io.meme) _read_motifs_meme_txt_regex() (in module sugar._io.meme) A add() (sugar.index.fastaindex.FastaIndex method) add_fts() (sugar.core.seq.BioBasket method) (sugar.core.seq.BioSeq method) append_fasta() (in module sugar._io.fasta) Attr (class in sugar.core.meta) B BETWEEN_CONSECUTIVE (sugar.core.fts.Defect attribute) BEYOND_LEFT (sugar.core.fts.Defect attribute) BEYOND_RIGHT (sugar.core.fts.Defect attribute) BioBasket (class in sugar.core.seq) BioMatch (class in sugar.core.cane) BioMatchList (class in sugar.core.cane) biopython2ft() (in module sugar.core._adapter) biopython2fts() (in module sugar.core._adapter) biopython2seq() (in module sugar.core._adapter) biopython2seqs() (in module sugar.core._adapter) BioSeq (class in sugar.core.seq) biotite2seq() (in module sugar.core._adapter) biotite2seqs() (in module sugar.core._adapter) C center() (sugar.core.seq._BioSeqStr method) complement() (sugar.core.seq.BioBasket method) (sugar.core.seq.BioSeq method) contains() (sugar.core.fts.Feature method) (sugar.core.fts.Location method) (sugar.core.fts.LocationTuple method) copy() (sugar.core.fts.FeatureList method) (sugar.core.meta.Attr method) (sugar.core.seq.BioBasket method) (sugar.core.seq.BioSeq method) count() (sugar.core.seq._BioSeqStr method) countall() (sugar.core.seq.BioBasket method) (sugar.core.seq.BioSeq method) countplot() (sugar.core.seq.BioBasket method) (sugar.core.seq.BioSeq method) D d (sugar.core.cane.BioMatchList property) (sugar.core.fts.FeatureList property) (sugar.core.seq.BioBasket property) data (sugar.core.seq.BioBasket attribute) (sugar.core.seq.BioSeq attribute) dbtype (sugar.index.fastaindex.FastaIndex property) Defect (class in sugar.core.fts) defect (sugar.core.fts.Location property) detect() (in module sugar._io.main) detect_ext() (in module sugar._io.main) distance() (sugar.core.fts.Feature method) (sugar.core.fts.Location method) (sugar.core.fts.LocationTuple method) E encode() (sugar.core.seq._BioSeqStr method) end() (sugar.core.cane.BioMatch method) endswith() (sugar.core.seq._BioSeqStr method) Entrez (class in sugar.web._entrez) extract_seqs() (in module sugar._io.tab.core) F FastaBinarySearchFile (class in sugar.index.fastaindex) FastaIndex (class in sugar.index.fastaindex) Feature (class in sugar.core.fts) FeatureList (class in sugar.core.fts) fetch_basket() (sugar.web._entrez.Entrez method) fetch_seq() (sugar.web._entrez.Entrez method) find() (sugar.core.seq._BioSeqStr method) find_orfs() (in module sugar.core.cane) (sugar.core.seq.BioBasket method) (sugar.core.seq.BioSeq method) FORWARD (sugar.core.fts.Strand attribute) frombiopython() (sugar.core.fts.Feature class method) (sugar.core.fts.FeatureList class method) (sugar.core.seq.BioBasket class method) (sugar.core.seq.BioSeq class method) frombiotite() (sugar.core.seq.BioBasket class method) (sugar.core.seq.BioSeq class method) fromfmtstr() (sugar.core.seq.BioBasket static method) frompandas() (sugar.core.fts.FeatureList class method) ft2biopython() (in module sugar.core._adapter) fts (sugar.core.seq.BioBasket property) (sugar.core.seq.BioSeq property) fts2biopython() (in module sugar.core._adapter) fts2row() (in module sugar._io.stockholm) G gc (sugar.core.seq.BioSeq property) gcode() (in module sugar.data) get() (sugar.core.fts.FeatureList method) get_basket() (sugar.index.fastaindex.FastaIndex method) (sugar.web._entrez.Entrez method) get_color_scheme() (in module sugar.imaging.colors) get_fasta() (sugar.index.fastaindex.FastaIndex method) get_fastaheader() (sugar.index.fastaindex.FastaIndex method) get_query_fts() (in module sugar._io.tab.core) get_seq() (sugar.index.fastaindex.FastaIndex method) (sugar.web._entrez.Entrez method) groupby() (sugar.core.cane.BioMatchList method) (sugar.core.fts.FeatureList method) (sugar.core.seq.BioBasket method) H headerstart (sugar.index.fastaindex.FastaBinarySearchFile attribute) I id (sugar.core.fts.Feature property) (sugar.core.seq.BioSeq property) ids (sugar.core.seq.BioBasket property) index() (sugar.core.seq._BioSeqStr method) is_clustal() (in module sugar._io.clustal) is_embl() (in module sugar._io.embl) is_fasta() (in module sugar._io.fasta) is_fts_blast() (in module sugar._io.tab.blast) is_fts_csv() (in module sugar._io.tab.xsv) is_fts_embl() (in module sugar._io.embl) is_fts_genbank() (in module sugar._io.genbank) is_fts_gff() (in module sugar._io.gff) is_fts_gtf() (in module sugar._io.gff) is_fts_infernal() (in module sugar._io.tab.infernal) is_fts_meme_txt() (in module sugar._io.meme) is_fts_mmseqs() (in module sugar._io.tab.mmseqs) is_fts_sjson() (in module sugar._io.sjson) is_fts_tsv() (in module sugar._io.tab.xsv) is_genbank() (in module sugar._io.genbank) is_gff() (in module sugar._io.gff) is_sjson() (in module sugar._io.sjson) is_stockholm() (in module sugar._io.stockholm) isalpha() (sugar.core.seq._BioSeqStr method) isascii() (sugar.core.seq._BioSeqStr method) islower() (sugar.core.seq._BioSeqStr method) isupper() (sugar.core.seq._BioSeqStr method) iter() (sugar.index.fastaindex.FastaIndex method) iter_() (in module sugar._io.main) iter_embl() (in module sugar._io.embl) iter_fasta() (in module sugar._io.fasta) (sugar.index.fastaindex.FastaIndex method) iter_fastaheader() (sugar.index.fastaindex.FastaIndex method) iter_genbank() (in module sugar._io.genbank) L ljust() (sugar.core.seq._BioSeqStr method) loc (sugar.core.fts.Feature property) loc_range (sugar.core.fts.FeatureList property) Location (class in sugar.core.fts) LocationTuple (class in sugar.core.fts) locs (sugar.core.fts.Feature property) lower() (sugar.core.seq._BioSeqStr method) lstrip() (sugar.core.seq._BioSeqStr method) M magic (sugar.index.fastaindex.FastaBinarySearchFile attribute) maketrans() (sugar.core.seq._BioSeqStr static method) match() (in module sugar.core.cane) (sugar.core.seq.BioBasket method) (sugar.core.seq.BioSeq method) matchall() (sugar.core.seq.BioBasket method) (sugar.core.seq.BioSeq method) merge() (sugar.core.seq.BioBasket method) Meta (class in sugar.core.meta) meta (sugar.core.fts.Location property) (sugar.core.seq.BioBasket attribute) (sugar.core.seq.BioSeq attribute) mid (sugar.core.fts.Location property) (sugar.core.fts.LocationTuple property) MISS_LEFT (sugar.core.fts.Defect attribute) MISS_RIGHT (sugar.core.fts.Defect attribute) module sugar._io sugar._io.clustal sugar._io.embl sugar._io.fasta sugar._io.genbank sugar._io.gff sugar._io.main sugar._io.meme sugar._io.sjson sugar._io.stockholm sugar._io.tab.blast sugar._io.tab.core sugar._io.tab.infernal sugar._io.tab.mmseqs sugar._io.tab.xsv sugar.core sugar.core._adapter sugar.core.cane sugar.core.fts sugar.core.meta sugar.core.seq sugar.data sugar.imaging sugar.imaging.alignment sugar.imaging.colors sugar.imaging.ftsviewer sugar.index sugar.index.fastaindex sugar.web sugar.web._entrez N name (sugar.core.fts.Feature property) NONE (sugar.core.fts.Defect attribute) (sugar.core.fts.Strand attribute) O ORFList (class in sugar.core.cane) overlaplen() (sugar.core.fts.Feature method) (sugar.core.fts.Location method) (sugar.core.fts.LocationTuple method) overlaps() (sugar.core.fts.Feature method) (sugar.core.fts.Location method) (sugar.core.fts.LocationTuple method) P plot_alignment() (in module sugar.imaging.alignment) (sugar.core.seq.BioBasket method) plot_ftsviewer() (in module sugar.imaging.ftsviewer) (sugar.core.fts.FeatureList method) (sugar.core.seq.BioBasket method) (sugar.core.seq.BioSeq method) R range (sugar.core.fts.Location property) (sugar.core.fts.LocationTuple property) rc() (sugar.core.fts.Feature method) (sugar.core.fts.FeatureList method) (sugar.core.seq.BioBasket method) (sugar.core.seq.BioSeq method) read() (in module sugar._io.main) read_clustal() (in module sugar._io.clustal) read_fts() (in module sugar._io.main) read_fts_blast() (in module sugar._io.tab.blast) read_fts_csv() (in module sugar._io.tab.xsv) read_fts_embl() (in module sugar._io.embl) read_fts_genbank() (in module sugar._io.genbank) read_fts_gff() (in module sugar._io.gff) read_fts_gtf() (in module sugar._io.gff) read_fts_infernal() (in module sugar._io.tab.infernal) read_fts_meme_txt() (in module sugar._io.meme) read_fts_mmseqs() (in module sugar._io.tab.mmseqs) read_fts_sjson() (in module sugar._io.sjson) read_fts_tsv() (in module sugar._io.tab.xsv) read_gff() (in module sugar._io.gff) read_sjson() (in module sugar._io.sjson) read_stockholm() (in module sugar._io.stockholm) read_tabular() (in module sugar._io.tab.core) record (sugar.index.fastaindex.FastaBinarySearchFile attribute) remove_duplicates() (sugar.core.fts.FeatureList method) remove_nested() (sugar.core.fts.FeatureList method) remove_overlapping() (sugar.core.fts.FeatureList method) removeprefix() (sugar.core.seq._BioSeqStr method) removesuffix() (sugar.core.seq._BioSeqStr method) replace() (sugar.core.seq._BioSeqStr method) REVERSE (sugar.core.fts.Strand attribute) reverse() (sugar.core.seq.BioBasket method) (sugar.core.seq.BioSeq method) rf (sugar.core.cane.BioMatch attribute) rfind() (sugar.core.seq._BioSeqStr method) rindex() (sugar.core.seq._BioSeqStr method) rjust() (sugar.core.seq._BioSeqStr method) row2fts() (in module sugar._io.stockholm) rsplit() (sugar.core.seq._BioSeqStr method) rstrip() (sugar.core.seq._BioSeqStr method) S scale_submat() (in module sugar.data) select() (sugar.core.cane.BioMatchList method) (sugar.core.fts.FeatureList method) (sugar.core.seq.BioBasket method) seq2biopython() (in module sugar.core._adapter) seq2biotite() (in module sugar.core._adapter) seqid (sugar.core.cane.BioMatch attribute) (sugar.core.fts.Feature property) seqs2biopython() (in module sugar.core._adapter) seqs2biotite() (in module sugar.core._adapter) setdefault() (sugar.core.meta.Attr method) shift() (sugar.core.fts.Location method) (sugar.core.fts.LocationTuple method) sl() (sugar.core.seq.BioBasket method) (sugar.core.seq.BioSeq method) slice() (sugar.core.fts.FeatureList method) slindex() (sugar.core.seq.BioSeq method) sort() (sugar.core.fts.FeatureList method) (sugar.core.seq.BioBasket method) span() (sugar.core.cane.BioMatch method) split() (sugar.core.seq._BioSeqStr method) splitlines() (sugar.core.seq._BioSeqStr method) start (sugar.core.fts.Location attribute) (sugar.core.fts.LocationTuple property) start() (sugar.core.cane.BioMatch method) startswith() (sugar.core.seq._BioSeqStr method) stop (sugar.core.fts.Location attribute) (sugar.core.fts.LocationTuple property) str (sugar.core.seq.BioBasket property) (sugar.core.seq.BioSeq property) Strand (class in sugar.core.fts) strand (sugar.core.fts.Location property) strip() (sugar.core.seq._BioSeqStr method) submat() (in module sugar.data) sugar._io module sugar._io.clustal module sugar._io.embl module sugar._io.fasta module sugar._io.genbank module sugar._io.gff module sugar._io.main module sugar._io.meme module sugar._io.sjson module sugar._io.stockholm module sugar._io.tab.blast module sugar._io.tab.core module sugar._io.tab.infernal module sugar._io.tab.mmseqs module sugar._io.tab.xsv module sugar.core module sugar.core._adapter module sugar.core.cane module sugar.core.fts module sugar.core.meta module sugar.core.seq module sugar.data module sugar.imaging module sugar.imaging.alignment module sugar.imaging.colors module sugar.imaging.ftsviewer module sugar.index module sugar.index.fastaindex module sugar.web module sugar.web._entrez module swapcase() (sugar.core.seq._BioSeqStr method) T tobiopython() (sugar.core.fts.Feature method) (sugar.core.fts.FeatureList method) (sugar.core.seq.BioBasket method) (sugar.core.seq.BioSeq method) tobiotite() (sugar.core.seq.BioBasket method) (sugar.core.seq.BioSeq method) todict() (sugar.core.fts.FeatureList method) (sugar.core.seq.BioBasket method) tofmtstr() (sugar.core.fts.FeatureList method) (sugar.core.seq.BioBasket method) (sugar.core.seq.BioSeq method) toftsviewer() (sugar.core.fts.Feature method) (sugar.core.fts.FeatureList method) (sugar.core.seq.BioSeq method) tolists() (sugar.core.fts.FeatureList method) topandas() (sugar.core.fts.FeatureList method) tostr() (sugar.core.cane.BioMatchList method) (sugar.core.fts.FeatureList method) (sugar.core.meta.Meta method) (sugar.core.seq.BioBasket method) (sugar.core.seq.BioSeq method) totalsize (sugar.index.fastaindex.FastaIndex property) translate() (in module sugar.core.cane) (sugar.core.seq._BioSeqStr method) (sugar.core.seq.BioBasket method) (sugar.core.seq.BioSeq method) type (sugar.core.fts.Feature property) (sugar.core.seq.BioSeq attribute) U UNKNOWN (sugar.core.fts.Strand attribute) UNKNOWN_LEFT (sugar.core.fts.Defect attribute) UNKNOWN_RIGHT (sugar.core.fts.Defect attribute) UNKNOWN_SINGLE_BETWEEN (sugar.core.fts.Defect attribute) update() (sugar.core.meta.Attr method) upper() (sugar.core.seq._BioSeqStr method) W write() (in module sugar._io.main) (sugar.core.fts.Feature method) (sugar.core.fts.FeatureList method) (sugar.core.seq.BioBasket method) (sugar.core.seq.BioSeq method) write_clustal() (in module sugar._io.clustal) write_fts() (in module sugar._io.main) write_fts_csv() (in module sugar._io.tab.xsv) write_fts_gff() (in module sugar._io.gff) write_fts_gtf() (in module sugar._io.gff) write_fts_sjson() (in module sugar._io.sjson) write_fts_tsv() (in module sugar._io.tab.xsv) write_gff() (in module sugar._io.gff) write_sjson() (in module sugar._io.sjson) write_stockholm() (in module sugar._io.stockholm)