README
¶
gfa
a Go library for working with Graphical Fragment Assembly format
Overview
This is a Go library for working with the Graphical Fragment Assembly (GFA) format.
The purpose of the GFA format is to capture sequence graphs as the product of an assembly, a representation of variation in genomes, splice graphs in genes, or even overlap between reads from long-read sequencing technology.
Read the GFA spec here.
Current limitations:
- restricted to GFA version 1
- does not handle the containment field
- validation is limited
Installation
go get github.com/will-rowe/gfa
Example usage
convert an MSA file to a GFA file
package main
import (
"log"
"os"
"github.com/will-rowe/gfa"
)
var (
inputFile = "./example.msa"
)
func main() {
// open the MSA
msa, _ := gfa.ReadMSA(inputFile)
// convert the MSA to a GFA instance
myGFA, err := gfa.MSA2GFA(msa)
if err != nil {
log.Fatal(err)
}
// create a gfaWriter
outfile, err := os.Create("./example.gfa")
defer outfile.Close()
writer, err := gfa.NewWriter(outfile, myGFA)
if err != nil {
log.Fatal(err)
}
// write the GFA content
if err := myGFA.WriteGFAContent(writer); err != nil {
log.Fatal(err)
}
}
process a GFA file line by line
package main
import (
"flag"
"io"
"log"
"os"
"github.com/will-rowe/gfa"
)
var (
inputFile = flag.String("inputFile", "", "input GFA file (empty for STDIN)")
)
func main() {
flag.Parse()
var r io.Reader
// open file stream and close it when finished
if *inputFile == "" {
r = os.Stdin
} else {
fh, err := os.Open(*inputFile)
if err != nil {
log.Fatalf("could not open file %q:", err)
}
defer fh.Close()
r = fh
}
// create a GFA reader
reader, err := gfa.NewReader(r)
if err != nil {
log.Fatal("can't read gfa file: %v", err)
}
// collect the GFA instance
myGFA := reader.CollectGFA()
// check version and print the header / comment lines
if myGFA.GetVersion() != 1 {
log.Fatal("gfa file is not in version 1 format")
}
log.Println(myGFA.PrintHeader())
if comments := myGFA.PrintComments(); comments != "" {
log.Println(comments)
}
// read the GFA file
for {
line, err := reader.Read()
if err == io.EOF {
break
}
if err != nil {
log.Fatal("error reading line in gfa file: %v", err)
}
// each line produced by Read() satisfies the gfaLine interface
formattedLine := line.PrintGFAline()
log.Printf("gfa line: %v", formattedLine)
// you can also add the line to the GFA instance
if err := line.Add(myGFA); err != nil {
log.Fatal("error adding line to GFA instance: %v", err)
}
}
}
Documentation
¶
Overview ¶
Package gfa is a Go library for working with the Graphical Fragment Assembly (GFA) format.
For more information:
GFA Format Specification https://github.com/GFA-spec/GFA-spec
This package currently only conforms to GFA1 spec.
Index ¶
- func NewLink(from, fOrient, to, tOrient, overlap []byte) (*link, error)
- func NewOptionalFields(optional ...[]byte) (*optionalFields, error)
- func NewPath(n []byte, segs, olaps [][]byte) (*path, error)
- func NewSegment(n, seq []byte) (*segment, error)
- func ReadMSA(fileName string) (*multi.Multi, error)
- type GFA
- func (gfa *GFA) AddComment(c []byte)
- func (gfa *GFA) AddVersion(v int) error
- func (gfa *GFA) GetLinks() ([]*link, error)
- func (gfa *GFA) GetPaths() ([]*path, error)
- func (gfa *GFA) GetSegments() ([]*segment, error)
- func (gfa *GFA) GetVersion() int
- func (gfa *GFA) MarshalHeader() []byte
- func (gfa *GFA) PrintComments() string
- func (gfa *GFA) PrintHeader() string
- func (gfa *GFA) PrintSequence(pathName []byte) ([]byte, error)
- func (gfa *GFA) Validate() error
- func (gfa *GFA) WriteGFAContent(w *GFAwriter) error
- type GFAwriter
- type Reader
Constants ¶
This section is empty.
Variables ¶
This section is empty.
Functions ¶
func NewOptionalFields ¶
NewOptionalFields is an optionalFields constructor
func NewSegment ¶
NewSegment is a segment constructor
Types ¶
type GFA ¶
type GFA struct {
// contains filtered or unexported fields
}
The GFA type holds all the information from a GFA formatted file
func (*GFA) AddComment ¶
AddComment appends a comment to the comments held by the GFA instance
func (*GFA) AddVersion ¶
AddVersion adds the GFA format version to the GFA instance
func (*GFA) GetSegments ¶
GetSegments returns a slice of all the segments held in the GFA instance
func (*GFA) GetVersion ¶
GetVersion returns the GFA version
// a return value of 0 indicates no version set
func (*GFA) MarshalHeader ¶
MarshalHeader prepares the header/comment lines for a writer
func (*GFA) PrintComments ¶
PrintComments prints a string of GFA formatted comment line(s)
func (*GFA) PrintHeader ¶
PrintHeader prints the GFA formatted header line
func (*GFA) PrintSequence ¶
PrintSequence will return the sequence encoded by a specified pathName
func (*GFA) Validate ¶
Validate performs several checks on the GFA instance TODO: add more checks
// checks that it contains a version (1/2)
// checks that is contains 1 or more segments
func (*GFA) WriteGFAContent ¶
WriteGFAContent will dump the content of a GFA instance to file
type GFAwriter ¶
type GFAwriter struct {
// contains filtered or unexported fields
}
GFAwriter implements GFA format writing
Source Files