sequtils

Nov 19, 2021

Changes in this version

+ func CreateFile(o string) (*bufio.Writer, *os.File, error)

+ func CreateFileGzip(o string) (*gzip.Writer, *os.File, error)

+ func OpenFastq(file string) (*bufio.Reader, *os.File, error)

type Fsq

+ func LoadNFastq(n int, r *bufio.Reader) (Fsq, bool, error)

+ func (f Fsq) WriteAppend(w *bufio.Writer) error

+ func (f Fsq) WriteAppendGzip(w *gzip.Writer) error

Nov 18, 2021

Changes in this version

type Fsq

+ func (f *Fsq) SearchIndex(i string, b, e int) error

Mar 19, 2021

Changes in this version

type Fna

+ func (f *Fna) HeaderFromConverter(c MapConverter) error

+ type MapConverter map[string]string

+ func LoadConverter(f string, flip bool) (MapConverter, error)

+ func NewMapConverter() MapConverter

+ func (c MapConverter) AddAssociation(o, n string) error

Mar 18, 2021

Changes in this version

+ func MatchFastaId(header, id, substr string) bool

+ func MatchFastqId(header, id, substr string) bool

Mar 16, 2021

Changes in this version

type Fsq

+ func (f *Fsq) FilterSequences(ids []string, idx SeqIndex, exact bool) error

+ func (f *Fsq) Swap(i, j int, sIdx SeqIndex)

Mar 14, 2021

Changes in this version

type Fna

+ func (f *Fna) FilterSequences(ids []string, idx SeqIndex, exact bool) error

+ func (f *Fna) Swap(i, j int, sIdx SeqIndex)

Mar 12, 2021

Changes in this version

type Fsq

+ func (f Fsq) WriteGzip(o string) error

Mar 11, 2021

Changes in this version

type Fastq

+ func NewFastq(h, s, q string) *Fastq

+ func (f *Fastq) GetQuality(phred64 bool) float64

+ func (f *Fastq) Rename(h string)

+ func (f *Fastq) Subsequence(s, e int) (*Fastq, error)

type Fsq

+ func LoadFastq(file string) (Fsq, error)

+ func NewFsq() Fsq

+ func (f *Fsq) AddFastq(seq *Fastq)

+ func (f *Fsq) FilterLength(min, max int)

+ func (f *Fsq) Get(r string, fIdx SeqIndex) (*Fastq, error)

+ func (f *Fsq) GetAvgQuality(phred bool) float64

+ func (f *Fsq) Index() (SeqIndex, error)

+ func (f Fsq) Write(o string, zip bool) error

+ type SeqIndex map[string]int

Feb 9, 2021

Changes in this version

type Fna

+ func (f *Fna) Get(r string, fIdx FastaIndex) (*Fasta, error)

Feb 3, 2021

Changes in this version

+ type Association struct

+ New string

+ Old string

+ type Converter []Association

+ func NewConverter(nb int) Converter

+ func (c *Converter) AddAssociation(idx int, old, new string) error

+ func (c Converter) ToCsv(o string) error

type Fna

+ func (f Fna) AddHeaderPrefix(h, d string) (Converter, error)

+ func (f Fna) AddHeaderSuffix(h, d string) (Converter, error)

+ func (f Fna) ReplaceHeader(h string) (Converter, error)

Jan 19, 2021

Changes in this version

type Fasta

+ func (f *Fasta) Rename(h string)

Jan 19, 2021

Changes in this version

type Fna

+ func NewFna() Fna

+ func (f *Fna) AddFasta(seq *Fasta)

Jan 19, 2021

Changes in this version

type Fna

+ func NewFasta() Fna

+ func (f *Fna) AddSequence(h, s string)

Jan 19, 2021

Changes in this version

+ type FastaIndex map[string]int

type Fna

+ func (f *Fna) Index() (FastaIndex, error)

Jan 17, 2021

Changes in this version

type Fasta

+ func (f *Fasta) Subsequence(s, e int) (*Fasta, error)

Jan 13, 2021

Changes in this version

+ func ExtractFna(file, prefix, taxid string, heads map[string]bool) error

+ func GetAvgQuality(input *os.File, output *os.File, phred bool) error

+ func GetFileType(inf *os.File) string

+ func Opener(inf, outf string) (*os.File, *os.File, error)

+ func ParseFastq(r *bufio.Scanner, phred64 bool) (float64, float64)

+ type Fasta struct

+ Header string

+ Sequence string

+ type Fastq struct

+ Quality string

+ Sep string

+ type Fna []*Fasta

+ func LoadFasta(file string) (Fna, error)

+ func (f *Fna) FilterLength(min, max int)

+ func (f Fna) Write(o string) error

+ type Fsq []*Fastq