Functions — github.com/citiususc/BigSeqKit

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Functions701 in github.com/citiususc/BigSeqKit

⨍ Functions 701◇ Types & classes 140

↓ 139 callersFunction_setDefault

(self, name, val)

bigseqkit-py/bigseqkit/helper.py:15

↓ 126 callersFunctionsetDefault

(pvar **T, val T)

bigseqkit/helper.go:41

↓ 74 callersFunctiongetFlagBool

(cmd *cobra.Command, flag string)

bigseqkit-cli/helper.go:268

↓ 48 callersFunctioncheckError

(err error)

bigseqkit-cli/helper.go:32

↓ 45 callersFunctioncheck

(e T, err error)

bigseqkit-cli/helper.go:25

↓ 42 callersFunctionlibSource

(name string)

bigseqkit/helper.go:21

↓ 40 callersFunction_config

(sq)

bigseqkit-py/bigseqkit/helper.py:46

↓ 35 callersFunction_libSource

(name)

bigseqkit-py/bigseqkit/helper.py:11

↓ 33 callersFunctiongetFlagString

(cmd *cobra.Command, flag string)

bigseqkit-cli/helper.go:274

↓ 27 callersMethodRead

()

bigseqkit-lib/helper.go:219

↓ 24 callersFunctionNewSeqParser

(t *seq.Alphabet, it iterator.IReadIterator[string], idRegexp string)

bigseqkit-lib/helper.go:179

↓ 23 callersFunctionOptionsToString

(v T)

bigseqkit/helper.go:47

↓ 23 callersFunctionaddCommand

(f func(*cobra.Command))

bigseqkit-cli/helper.go:21

↓ 23 callersFunctionignisDriver

(cmd *cobra.Command, args []string, f func(input []*api.IDataFrame[string], cmd *cobra.Command, args []string

bigseqkit-cli/helper.go:87

↓ 22 callersMethodConfig

(v *SeqKitConfig)

bigseqkit/seq.go:57

↓ 22 callersMethodGetAlphabet

()

bigseqkit/helper.go:68

↓ 22 callersFunctionparseSeqKitConfig

(cmd *cobra.Command)

bigseqkit-cli/helper.go:143

↓ 21 callersFunction_optionsToString

(v)

bigseqkit-py/bigseqkit/helper.py:30

↓ 20 callersFunction_parseKargs

(obj, kwargs)

bigseqkit-py/bigseqkit/helper.py:34

↓ 19 callersFunctionunion

(cmd *cobra.Command, input ...*api.IDataFrame[string])

bigseqkit-cli/helper.go:134

↓ 14 callersMethodAlphabet

()

bigseqkit-lib/helper.go:371

↓ 8 callersFunctiongetFlagInt

(cmd *cobra.Command, flag string)

bigseqkit-cli/helper.go:244

↓ 8 callersFunctiongetFlagNonNegativeInt

(cmd *cobra.Command, flag string)

bigseqkit-cli/helper.go:259

↓ 7 callersMethodIgnoreCase

(v bool)

bigseqkit/sort.go:81

↓ 7 callersFunctiongetFlagPositiveInt

(cmd *cobra.Command, flag string)

bigseqkit-cli/helper.go:250

↓ 5 callersMethodByName

(v bool)

bigseqkit/sort.go:56

↓ 5 callersMethodBySeq

(v bool)

bigseqkit/sort.go:51

↓ 5 callersMethodHasNext

()

bigseqkit-lib/helper.go:147

↓ 5 callersMethodNext

()

bigseqkit-lib/helper.go:151

↓ 5 callersMethodOnlyPositiveStrand

(v bool)

bigseqkit/grep.go:91

↓ 5 callersFunctiongetFlagStringSlice

(cmd *cobra.Command, flag string)

bigseqkit-cli/helper.go:292

↓ 4 callersFunctionNewArrayIterator

(array []string)

bigseqkit-lib/helper.go:138

↓ 4 callersFunctionfixer

(input *api.IDataFrame[string], delim string)

bigseqkit/helper.go:140

↓ 4 callersFunctionparseHeadID

(head []byte, isUsingDefaultIDRegexp bool)

bigseqkit-lib/faidx.go:434

↓ 3 callersMethodPattern

(v []string)

bigseqkit/grep.go:56

↓ 3 callersMethodRange

(v string)

bigseqkit/range.go:31

↓ 3 callersMethodUseRegexp

(v bool)

bigseqkit/grep.go:66

↓ 3 callersFunctiongetFileListFromArgsAndFile

(cmd *cobra.Command, args []string, checkFileFromArgs bool, flag string, checkFileFromFile bool)

bigseqkit-cli/helper.go:229

↓ 3 callersFunctiongetFlagFloat64

(cmd *cobra.Command, flag string)

bigseqkit-cli/helper.go:280

↓ 3 callersFunctiongetFlagInt64

(cmd *cobra.Command, flag string)

bigseqkit-cli/helper.go:286

↓ 3 callersFunctionmergeBytes

(aa ...[]byte)

bigseqkit-lib/helper.go:68

↓ 2 callersMethodBed

(v bool)

bigseqkit/locate.go:102

↓ 2 callersMethodCircular

(v bool)

bigseqkit/grep.go:116

↓ 2 callersMethodDegenerate

(v bool)

bigseqkit/grep.go:106

↓ 2 callersMethodGapLetters

bigseqkit/locate.go:97

↓ 2 callersMethodMaxMismatch

(v int)

bigseqkit/grep.go:96

↓ 2 callersFunctionParser

()

bigseqkit-cli/helper.go:153

↓ 2 callersMethodPatternFile

(v string)

bigseqkit/grep.go:61

↓ 2 callersFunctionReadBedFilteredFeatures

ReadBedFilteredFeatures returns gtf BedFeatures of selected chrs from file

bigseqkit-lib/subseq.go:242

↓ 2 callersMethodRegion

(v string)

bigseqkit/grep.go:111

↓ 2 callersMethodReverse

(v bool)

bigseqkit/seq.go:62

↓ 2 callersMethodSeed

(v int)

bigseqkit/sample.go:33

↓ 2 callersMethodSeq

(v bool)

bigseqkit/seq.go:77

↓ 2 callersFunction_fixer

(input: IDataFrame, delim: str)

bigseqkit-py/bigseqkit/helper.py:106

↓ 2 callersMethod_prepareCommon

(self, inputA: IDataFrame, id: str)

bigseqkit-py/bigseqkit/common.py:24

↓ 2 callersMethod_prepareConcat

(self, inputA: IDataFrame, id: str)

bigseqkit-py/bigseqkit/concat.py:18

↓ 2 callersFunctioncommonGrep

(input *api.IDataFrame[string], opts *GrepOptions)

bigseqkit/grep.go:121

↓ 2 callersMethodcount

(self, v: bool)

bigseqkit-py/bigseqkit/grep.py:53

↓ 2 callersFunctiondropCR

(data []byte)

bigseqkit-lib/faidx.go:452

↓ 2 callersFunctionextension

(s string, es []string)

bigseqkit-cli/helper.go:38

↓ 2 callersMethodparseHeadIDAndDesc

(idRegexp *regexp.Regexp, head []byte)

bigseqkit-lib/helper.go:329

↓ 2 callersFunctionprepareCommon

(input *api.IDataFrame[string], opts *CommonOptions, id string)

bigseqkit/common.go:56

↓ 2 callersFunctionprepareConcat

(input *api.IDataFrame[string], opts *ConcatOptions, id string)

bigseqkit/concat.go:41

↓ 2 callersFunctionpreparePair

(input *api.IDataFrame[string], opts *PairOptions, id string)

bigseqkit/pair.go:34

↓ 2 callersFunctionrange

(input: IDataFrame, o: SeqKitRangeOptions = None, **kwargs)

bigseqkit-py/bigseqkit/range.py:66

↓ 2 callersFunctionreadSeqs

(cmd *cobra.Command, args []string, pipe bool)

bigseqkit-cli/helper.go:47

↓ 2 callersMethodsetDefaults

()

bigseqkit/stats.go:28

↓ 2 callersMethodsetDefaults

()

bigseqkit/grep.go:31

↓ 2 callersFunctionwrapByteSlice

(s []byte, width int, buffer *bytes.Buffer)

bigseqkit-lib/helper.go:81

↓ 1 callersMethodAll

(v bool)

bigseqkit/stats.go:55

↓ 1 callersMethodAllowUnknownCodon

(v bool)

bigseqkit/translate.go:62

↓ 1 callersMethodAlphabetGuessSeqLength

(v int)

bigseqkit/helper.go:130

↓ 1 callersMethodAppendFrame

(v bool)

bigseqkit/translate.go:82

↓ 1 callersMethodByBases

(v bool)

bigseqkit/sort.go:66

↓ 1 callersMethodByLength

bigseqkit/subseq.go:42

↓ 1 callersMethodClean

(v bool)

bigseqkit/translate.go:57

↓ 1 callersMethodComplement

(v bool)

bigseqkit/seq.go:67

↓ 1 callersMethodDeleteMatched

(v bool)

bigseqkit/grep.go:71

↓ 1 callersMethodDna2rna

(v bool)

bigseqkit/seq.go:112

↓ 1 callersMethodDownStream

(v int)

bigseqkit/subseq.go:67

↓ 1 callersMethodDupNumFile

(v string)

bigseqkit/rmdup.go:60

↓ 1 callersMethodDupSeqsFile

(v string)

bigseqkit/rmdup.go:55

↓ 1 callersMethodFastaFile

(v string)

bigseqkit/fa2fq.go:30

↓ 1 callersMethodFeature

(v []string)

bigseqkit/subseq.go:57

↓ 1 callersMethodFrame

(v []string)

bigseqkit/translate.go:47

↓ 1 callersMethodFull

(v bool)

bigseqkit/concat.go:31

↓ 1 callersMethodFullHead

(v bool)

bigseqkit/faidx.go:46

↓ 1 callersMethodGtfTag

(v string)

bigseqkit/subseq.go:82

↓ 1 callersMethodHideMatched

(v bool)

bigseqkit/locate.go:112

↓ 1 callersMethodIDNCBI

(self, v: bool)

bigseqkit-py/bigseqkit/helper.py:64

↓ 1 callersMethodIDRegexp

(self, v: str)

bigseqkit-py/bigseqkit/helper.py:61

↓ 1 callersMethodInNaturalOrder

(v bool)

bigseqkit/sort.go:46

↓ 1 callersMethodInitCodonAsM

(v bool)

bigseqkit/translate.go:67

↓ 1 callersMethodInvertMatch

(v bool)

bigseqkit/grep.go:76

↓ 1 callersMethodKeepKey

(v bool)

bigseqkit/replace.go:79

↓ 1 callersMethodKeepUntouch

(v bool)

bigseqkit/replace.go:74

↓ 1 callersMethodKeyCaptIdx

(v int)

bigseqkit/replace.go:84

↓ 1 callersMethodKeyMissRepl

(v string)

bigseqkit/replace.go:89

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