align

Nov 6, 2023

Changes in this version

type Alignment

+ ReplaceChar func(seqname string, site int, newchar uint8) error

+ TranslateByReference func(phase int, geneticcode int, refseq string) (err error)

type SeqBag

+ GetSequenceIdByName func(name string) (i int)

Nov 17, 2022

Changes in this version

+ type Mutation struct

+ Alt uint8

+ Pos int

+ Ref uint8

type Sequence

+ ListMutationsComparedToReferenceSequence func(alphabet int, refseq Sequence) (mutations []Mutation, err error)

May 4, 2021

Changes in this version

+ const IGNORE_NAME

+ const IGNORE_NONE

+ const IGNORE_SEQUENCE

+ const NT_A

+ const NT_B

+ const NT_C

+ const NT_D

+ const NT_G

+ const NT_H

+ const NT_K

+ const NT_M

+ const NT_N

+ const NT_OTHER

+ const NT_R

+ const NT_S

+ const NT_T

+ const NT_V

+ const NT_W

+ const NT_Y

+ var IupacCode = map[uint8][]uint8

+ func EqualOrCompatible(nt1, nt2 uint8) (ok bool, err error)

+ func GenAllPossibleCodons(nt1, nt2, nt3 uint8) (codons []string)

+ func Nt2IndexIUPAC(nt uint8) (idx uint8, err error)

+ func NtIUPACDifference(nt1, nt2 uint8) (diff float64, err error)

+ func PossibleNtIUPAC(nt uint8) (idx []uint8, err error)

type Alignment

+ Append func(Alignment) error

+ Consensus func(ignoreGaps, ignoreNs bool) *align

+ InformativeSites func() (sites []int)

+ InverseCoordinates func(start, length int) (invstarts, invlengths []int, err error)

+ InversePositions func(sites []int) (invsites []int, err error)

+ MaskOccurences func(refseq string, maxOccurence int, maskreplace string) error

+ MaskUnique func(refseq string, maskreplace string) error

+ NumGapsUniquePerSequence func(countProfile *CountProfile) (numuniques []int, numnew []int, numboth []int, err error)

+ NumMutationsUniquePerSequence func(profile *CountProfile) (numuniques []int, numnew []int, nummuts []int, err error)

+ RefCoordinates func(name string, refstart, refend int) (alistart, aliend int, err error)

+ RefSites func(name string, sites []int) (refsites []int, err error)

+ RemoveCharacterSeqs func(c uint8, cutoff float64, ignoreCase, ignoreGaps, ignoreNs bool) int

+ RemoveCharacterSites func(c uint8, cutoff float64, ends bool, ignoreCase, ignoreGaps, ignoreNs bool) (first, last int, kept []int)

+ RemoveMajorityCharacterSites func(cutoff float64, ends, ignoreGaps, ignoreNs bool) (first, last int, kept []int)

+ SelectSites func(sites []int) (Alignment, error)

+ Transpose func() (Alignment, error)

+ type CountProfile struct

+ func NewCountProfile() (p *CountProfile)

+ func NewCountProfileFromAlignment(al Alignment) (p *CountProfile)

+ func (p *CountProfile) AppendCount(i, count int) (err error)

+ func (p *CountProfile) CheckLength(length int) bool

+ func (p *CountProfile) Count(r uint8, site int) (count int, err error)

+ func (p *CountProfile) CountAt(i, site int) (count int, err error)

+ func (p *CountProfile) CountsAt(i int) (counts []int, err error)

+ func (p *CountProfile) NameAt(i int) (name uint8, err error)

+ func (p *CountProfile) NameIndex(r uint8) (index int, ok bool)

+ func (p *CountProfile) NbCharacters() (nb int)

+ func (p *CountProfile) Print()

+ func (p *CountProfile) SetHeader(header []uint8)

type SeqBag

+ CharStatsSeq func(idx int) (map[uint8]int, error)

+ FilterLength func(minlength, maxlength int) error

+ GetSequenceByName func(name string) (Sequence, bool)

+ RarefySeqBag func(nb int, counts map[string]int) (SeqBag, error)

+ ReverseComplement func() (err error)

+ SampleSeqBag func(nb int) (SeqBag, error)

+ UniqueCharacters func() []uint8

type Sequence

+ NumGaps func() int

+ NumGapsFromEnd func() int

+ NumGapsFromStart func() int

+ NumGapsOpenning func() int

+ NumMutationsComparedToReferenceSequence func(alphabet int, seq Sequence) (nummutations int, err error)

Jan 14, 2020

Changes in this version

type Alignment

+ Split func(part *PartitionSet) ([]Alignment, error)

+ type PartitionSet struct

+ func NewPartitionSet(alignmentLength int) (ps *PartitionSet)

+ func (ps *PartitionSet) AddRange(partName, modelName string, start, end, modulo int) (err error)

+ func (ps *PartitionSet) AliLength() int

+ func (ps *PartitionSet) CheckSites() (err error)

+ func (ps *PartitionSet) ModeleName(code int) string

+ func (ps *PartitionSet) NPartitions() int

+ func (ps *PartitionSet) Partition(position int) int

+ func (ps *PartitionSet) PartitionName(code int) string

+ func (ps *PartitionSet) String() string

Sep 30, 2019

Changes in this version

+ const GENETIC_CODE_INVETEBRATE_MITO

+ const GENETIC_CODE_STANDARD

+ const GENETIC_CODE_VETEBRATE_MITO

+ func AA2Index(aa rune) (idx int, err error)

+ func Index2AA(index int) (aa rune, err error)

+ func Index2Nt(index int) (nt rune, err error)

+ func Nt2Index(nt rune) (idx int, err error)

type Alignment

+ Compress func() []int

+ CountDifferences func() (alldiffs []string, diffs []map[string]int)

+ DiffWithFirst func()

+ ReplaceMatchChars func()

type Phaser

+ SetGapExtend func(float64)

+ SetGapOpen func(float64)

type SeqBag

+ AlphabetCharToIndex func(c rune) int

+ IgnoreIdentical func(bool)

type Sequence

+ SameSequence func([]rune) bool

Mar 11, 2019

Changes in this version

+ const ALIGN_ALGO_ATG

+ const ALIGN_ALGO_SW

+ const ALIGN_DIAG

+ const ALIGN_LEFT

+ const ALIGN_STOP

+ const ALIGN_UP

+ const ALL_AMINO

+ const ALL_NUCLE

+ const BOTH

+ func Complement(seq []rune) (err error)

+ func NewPwAligner(seq1, seq2 Sequence, algo int) *pwaligner

+ func NewSeqBag(alphabet int) *seqbag

+ func Reverse(seq []rune)

type Alignment

+ CodonAlign func(ntseqs SeqBag) (codonAl *align, err error)

+ Frameshifts func(startingGapsAsIncomplete bool) []struct{ ... }

+ Mask func(start, length int) error

+ Stops func(startingGapsAsIncomplete bool) []int

+ type PairwiseAligner interface

+ AlignEnds func() (int, int)

+ AlignStarts func() (int, int)

+ Alignment func() (Alignment, error)

+ AlignmentStr func() string

+ Length func() int

+ MaxScore func() float64

+ NbGaps func() int

+ NbMatches func() int

+ NbMisMatches func() int

+ Seq1Ali func() []rune

+ Seq2Ali func() []rune

+ SetGapExtendScore func(extend float64)

+ SetGapOpenScore func(open float64)

+ SetScore func(match, mismatch float64)

+ type PhasedSequence struct

+ AaSeq Sequence

+ Ali Alignment

+ CodonSeq Sequence

+ Err error

+ NtSeq Sequence

+ Position int

+ Removed bool

+ type Phaser interface

+ Phase func(orfs, seqs SeqBag) (chan PhasedSequence, error)

+ SetAlignScores func(match, mismatch float64)

+ SetCpus func(cpus int)

+ SetCutEnd func(cutend bool)

+ SetLenCutoff func(cutoff float64)

+ SetMatchCutoff func(cutoff float64)

+ SetReverse func(reverse bool)

+ SetTranslate func(translate bool)

+ func NewPhaser() Phaser

+ type SeqBag interface

+ AddSequence func(name string, sequence string, comment string) error

+ AddSequenceChar func(name string, sequence []rune, comment string) error

+ Alphabet func() int

+ AlphabetCharacters func() []rune

+ AlphabetStr func() string

+ AppendSeqIdentifier func(identifier string, right bool)

+ AutoAlphabet func()

+ CharStats func() map[rune]int64

+ CleanNames func(namemap map[string]string)

+ Clear func()

+ CloneSeqBag func() (seqs SeqBag, err error)

+ Deduplicate func() error

+ GetSequence func(name string) (string, bool)

+ GetSequenceById func(ith int) (string, bool)

+ GetSequenceChar func(name string) ([]rune, bool)

+ GetSequenceCharById func(ith int) ([]rune, bool)

+ GetSequenceNameById func(ith int) (string, bool)

+ Identical func(SeqBag) bool

+ Iterate func(it func(name string, sequence string))

+ IterateAll func(it func(name string, sequence []rune, comment string))

+ IterateChar func(it func(name string, sequence []rune))

+ LongestORF func(reverse bool) (orf Sequence, err error)

+ MaxNameLength func() int

+ NbSequences func() int

+ Rename func(namemap map[string]string)

+ RenameRegexp func(regex, replace string, namemap map[string]string) error

+ Replace func(old, new string, regex bool) error

+ Sequence func(ith int) (Sequence, bool)

+ SequenceByName func(name string) (Sequence, bool)

+ Sequences func() []Sequence

+ SequencesChan func() chan Sequence

+ SetSequenceChar func(ithAlign, ithSite int, char rune) error

+ ShuffleSequences func()

+ Sort func()

+ String func() string

+ Translate func(phase int) (err error)

+ TrimNames func(namemap map[string]string, size int) error

+ TrimNamesAuto func(namemap map[string]string, curid *int) error

+ Unalign func() SeqBag

type Sequence

+ CharAt func(int) rune

+ Clone func() Sequence

+ Complement func() error

+ DetectAlphabet func() int

+ Length func() int

+ LongestORF func() (start, end int)

+ Reverse func()

+ SetName func(name string)

+ Translate func(phase int) (Sequence, error)

Jul 4, 2018

Changes in this version

+ const FORMAT_CLUSTAL

+ const POSITION_CONSERVED

+ const POSITION_IDENTICAL

+ const POSITION_NOT_CONSERVED

+ const POSITION_SEMI_CONSERVED

type Alignment

+ CharStatsSite func(site int) (map[rune]int, error)

+ MaxCharStats func() ([]rune, []int)

+ RenameRegexp func(regex, replace string, namemap map[string]string) error

+ SiteConservation func(position int) (int, error)

+ Translate func(phase int) (transAl *align, err error)

Jan 26, 2018

Changes in this version

type Alignment

+ CleanNames func()

+ TrimNamesAuto func() (map[string]string, error)

Nov 27, 2017

Changes in this version

+ const FORMAT_FASTA

+ const FORMAT_NEXUS

+ const FORMAT_PHYLIP

+ type AlignChannel struct

+ Achan chan Alignment

+ Err error

Oct 13, 2017

Changes in this version

+ const UNKNOWN

+ func AlphabetFromString(alphabet string) int

type Alignment

+ GetSequenceById func(ith int) (string, bool)

+ GetSequenceCharById func(ith int) ([]rune, bool)

+ GetSequenceNameById func(ith int) (string, bool)

+ Rarefy func(nb int, counts map[string]int) (Alignment, error)

+ RemoveGapSeqs func(cutoff float64)

+ RemoveGapSites func(cutoff float64)

+ Sort func()

Jul 3, 2017

Changes in this version

type Alignment

+ NbVariableSites func() int

Jun 20, 2017

Changes in this version

type Alignment

+ Mutate func(rate float64)

Jun 8, 2017

Changes in this version

type Alignment

+ AddGaps func(rate, lenprop float64)

Apr 14, 2017

Changes in this version

type Alignment

+ Concat func(Alignment) error

+ RandSubAlign func(length int) (Alignment, error)

Apr 7, 2017

Changes in this version

+ const POINT

+ const PSSM_NORM_LOGO

type Alignment

+ SubAlign func(start, length int) (Alignment, error)

Mar 27, 2017

Changes in this version

+ const PSSM_NORM_DATA

+ const PSSM_NORM_FREQ

+ const PSSM_NORM_NONE

+ const PSSM_NORM_UNIF

type Alignment

+ AlphabetCharacters func() []rune

+ Pssm func(log bool, pseudocount float64, normalization int) (pssm map[rune][]float64, err error)

Mar 15, 2017

Changes in this version

+ const OTHER

type Alignment

+ Entropy func(site int) (float64, error)

+ SetSequenceChar func(ithAlign, ithSite int, char rune) error

+ SimulateRogue func(prop float64, proplen float64) ([]string, []string)

Feb 28, 2017

Changes in this version

type Alignment

+ Rename func(namemap map[string]string)

Feb 10, 2017

Changes in this version

+ const GAP

type Alignment

+ AvgAllelesPerSite func() float64

+ Clone func() (Alignment, error)

+ IterateAll func(it func(name string, sequence []rune, comment string))

+ RemoveGaps func(all bool)

Jan 26, 2017

Changes in this version

+ func RandomSequence(alphabet, length int) ([]rune, error)

type Alignment

+ func RandomAlignment(alphabet, length, nbseq int) (Alignment, error)

+ AppendSeqIdentifier func(identifier string, right bool)

Oct 14, 2016

Changes in this version

type Alignment

+ AddSequenceChar func(name string, sequence []rune, comment string) error

+ Alphabet func() int

+ CharStats func() map[rune]int64

+ GetSequenceChar func(ith int) ([]rune, bool)

+ GetSequenceName func(ith int) (string, bool)

+ IterateChar func(it func(name string, sequence []rune))

+ Swap func(rate float64)

+ TrimNames func(size int) (map[string]string, error)

+ TrimSequences func(trimsize int, fromStart bool) error

type Sequence

+ SequenceChar func() []rune

Aug 25, 2016

Changes in this version

+ const AMINOACIDS

+ const NUCLEOTIDS

+ func DetectAlphabet(seq string) int

+ func NewAlign(alphabet int) *align

+ func NewSequence(name string, sequence string, comment string) *seq

+ type Alignment interface

+ AddSequence func(name string, sequence string, comment string) error

+ BuildBootstrap func() Alignment

+ GetSequence func(name string) (string, bool)

+ Iterate func(it func(name string, sequence string))

+ Length func() int

+ NbSequences func() int

+ Recombine func(rate float64)

+ Sample func(nb int) (Alignment, error)

+ ShuffleSequences func()

+ ShuffleSites func(rate float64)

+ type Sequence interface

+ Comment func()

+ Name func()

+ Sequence func()