gofasta

package module

v0.0.0-...-e776ef6 Latest Latest Go to latest Published: Apr 7, 2015 License: MIT Imports: 8 Imported by: 7

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

github.com/aebruno/gofasta

Links

Open Source Insights

README ¶

===============================================================================
gofasta - Process FASTA files in Go
===============================================================================

-------------------------------------------------------------------------------
About
-------------------------------------------------------------------------------

gofasta is library for processing FASTA [1] files and extracting sequences from
indexed FASTA files in faidx [2] format. 

-------------------------------------------------------------------------------
Install
-------------------------------------------------------------------------------

Fetch from github::

    $ go get github.com/aebruno/gofasta/...

-------------------------------------------------------------------------------
Usage
-------------------------------------------------------------------------------

Extract sequences from indexed fasta file::

    $ faidx /genomes/hg19.fa chr1:1000-100000

Cat FASTA files::

    $ fastcat -fasta test.fasta --count
    $ fastcat --help
    Usage of fastcat:
      -count=false: count sequences
      -fasta="": path to FASTA file
      -id=false: output ids
      -seq=false: output sequences

-------------------------------------------------------------------------------
References
-------------------------------------------------------------------------------

[1] http://en.wikipedia.org/wiki/FASTA_format 

[2] http://samtools.sourceforge.net/samtools.shtml

Documentation ¶

Index ¶

func SimpleParser(file *os.File) chan *SeqRecord
type Faidx
- func NewFaidx(fileName string) (*Faidx, error)
- func (f *Faidx) Close() error
- func (f *Faidx) Fetch(chr string, start, end int) ([]byte, error)
type SeqRecord

Constants ¶

This section is empty.

Variables ¶

This section is empty.

Functions ¶

func SimpleParser ¶

func SimpleParser(file *os.File) chan *SeqRecord

Types ¶

type Faidx ¶

type Faidx struct {
	IndexCache map[string][]int64
	// contains filtered or unexported fields
}

func NewFaidx ¶

func NewFaidx(fileName string) (*Faidx, error)

func (*Faidx) Close ¶

func (f *Faidx) Close() error

func (*Faidx) Fetch ¶

func (f *Faidx) Fetch(chr string, start, end int) ([]byte, error)

type SeqRecord ¶

type SeqRecord struct {
	Id  string
	Seq string
}

Source Files ¶

View all Source files

Directories ¶

Path	Synopsis
cmd
faidx
fastcat

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