sequtils

package module

v0.9.2 Latest Latest Go to latest Published: Feb 4, 2021 License: MIT Imports: 9 Imported by: 1

Details

Valid go.mod file

The Go module system was introduced in Go 1.11 and is the official dependency management solution for Go.
Redistributable license

Redistributable licenses place minimal restrictions on how software can be used, modified, and redistributed.
Tagged version

Modules with tagged versions give importers more predictable builds.
Stable version

When a project reaches major version v1 it is considered stable.
Learn more about best practices

Repository

bitbucket.org/GottySG36/sequtils

Links

Open Source Insights

Documentation ¶

Overview ¶

Sets of utilities to parse Fastq/a files

Index ¶

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 Association
type Converter
- func NewConverter(nb int) Converter
- func (c *Converter) AddAssociation(idx int, old, new string) error
- func (c *Converter) ToCsv(o string) error
type Fasta
- func NewFasta(h, s string) *Fasta
- func (f *Fasta) Rename(h string)
- func (f *Fasta) Subsequence(s, e int) (*Fasta, error)
type FastaIndex
type Fastq
type Fna
- func LoadFasta(file string) (Fna, error)
- func NewFna() Fna
type Fsq

Constants ¶

This section is empty.

Variables ¶

This section is empty.

Functions ¶

func ExtractFna ¶

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

Could be merged / removed because it can be accomplished with combination of simpler function/methods combination Load, Index, NewFasta, AddSequence, Write

func GetAvgQuality ¶

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

GetAvgQuality takes an fastq file and attempts to calculate the average sequence quality and the sequence count. Utilises phred33 representation. usage : GetAvgQuality(<input>, <output>) Keyword arguments: input : File pointer (*os.File()), input data, either gunzipped or plain text. output : File pointer, output data containing the average quality and sequence count.

If output is nil, writes to Stdout

Return: None : Directly writes to file or Stdout

func GetFileType ¶

func GetFileType(inf *os.File) string

func Opener ¶

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

func ParseFastq ¶

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

Types ¶

type Association ¶ added in v0.9.0

type Association struct {
	Old string
	New string
}

Type used to keep track of old and new header names. For use with Replace, AddHeaderPrefix and AddHeaderSuffix

type Converter ¶ added in v0.9.0

type Converter []*Association

func NewConverter ¶ added in v0.9.0

func NewConverter(nb int) Converter

Convenience method to create a new converter and allocate enough space for `nb` Associations

func (*Converter) AddAssociation ¶ added in v0.9.0

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

Adds an `Association` to the converter, replacing any existing one at position `idx` Return an error if `idx >= len(c)`

func (*Converter) ToCsv ¶ added in v0.9.0

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

type Fasta ¶

type Fasta struct {
	Header   string
	Sequence string
}

func NewFasta ¶ added in v0.8.0

func NewFasta(h, s string) *Fasta

function to create a fasta struct from two strings Take two arguments, 1. h : The header to use (will automatically add the starting '>') 2. s : The sequence itself.

func (*Fasta) Rename ¶ added in v0.8.2

func (f *Fasta) Rename(h string)

Changes the header to `h`

func (*Fasta) Subsequence ¶ added in v0.6.0

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

type FastaIndex ¶ added in v0.7.0

type FastaIndex map[string]int

type Fastq ¶

type Fastq struct {
	Fasta
	Sep     string
	Quality string
}

type Fna ¶

type Fna []*Fasta

func LoadFasta ¶

func LoadFasta(file string) (Fna, error)

func NewFna ¶ added in v0.8.1

func NewFna() Fna

Convinience function to create a Fna struct

func (*Fna) AddFasta ¶ added in v0.8.1

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

Convinience method to add a fasta struct to the Fna

func (*Fna) AddHeaderPrefix ¶ added in v0.9.0

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

Adds prefix `h` to the sequences' header seperating both by delimiter `d` Return the associated Converter and an error.

func (*Fna) AddHeaderSuffix ¶ added in v0.9.0

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

Adds prefix `h` to the sequences' header seperating both by delimiter `d` Return the associated Converter and an error.

func (*Fna) FilterLength ¶

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

Simple Utility to filter the lengths of fasta sequences. Iterates over a slice of Sequences (Fna) and filters out the sequences whose lengths are lower or greater than the specified mininimum and maximum. If maximum <= 0, max is set to the length of the sequence. Returns filtered Fna

func (*Fna) Index ¶ added in v0.7.0

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

Index the loaded fasta file using fasta headers Assumes that all headers are unique, raises an error if not

func (*Fna) ReplaceHeader ¶ added in v0.9.0

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

Replaces all existing headers by `h` follow by a sequential number Return the associated Converter and an error.

func (Fna) Write ¶

func (f Fna) Write(o string) error

type Fsq ¶

type Fsq []*Fastq

Source Files ¶

View all Source files

sequtils.go

?	: This menu
/	: Search site
f or F	: Jump to
y or Y	: Canonical URL