Documentation
¶
Overview ¶
Package fastq contains fastq parsers and writers.
Fastq is a flat text file format developed in ~2000 to store nucleotide sequencing data. While similar to fastq, fastq has a few differences. First, the sequence identifier begins with @ instead of >, and includes quality values for a sequence.
This package provides a parser and writer for working with Fastq formatted sequencing data.
Index ¶
Examples ¶
Constants ¶
This section is empty.
Variables ¶
This section is empty.
Functions ¶
This section is empty.
Types ¶
type Header ¶
type Header struct{}
Header is a blank struct, needed for compatibility with bio parsers. It contains nothing.
type Parser ¶
type Parser struct {
// contains filtered or unexported fields
}
Parser is a flexible parser that provides ample control over reading fastq-formatted sequences. It is initialized with NewParser.
Example ¶
package main
import (
_ "embed"
"fmt"
"strings"
"github.com/koeng101/dnadesign/lib/bio/fastq"
)
//go:embed data/nanosavseq.fastq
var baseFastq string
func main() {
parser := fastq.NewParser(strings.NewReader(baseFastq), 2*32*1024)
for {
fastq, err := parser.Next()
if err != nil {
fmt.Println(err)
break
}
fmt.Println(fastq.Identifier)
}
}
Output: e3cc70d5-90ef-49b6-bbe1-cfef99537d73 92728f25-b658-426c-8cd7-d82dc70dbf71 60907b6b-5e38-498e-9c07-f036ebd8c658 990e110e-5e50-41a2-8ad5-92044d4465b8 EOF
func NewParser ¶
NewParser returns a Parser that uses r as the source from which to parse fastq formatted sequences.
func (*Parser) Next ¶
Next reads next fastq genome in underlying reader and returns the result and the amount of bytes read during the call. Next only returns an error if it:
- Attempts to read and fails to find a valid fastq sequence.
- Returns reader's EOF if called after reader has been exhausted.
- If a EOF is encountered immediately after a sequence with no newline ending. In this case the Read up to that point is returned with an EOF error.
It is worth noting the amount of bytes read are always right up to before the next fastq starts which means this function can effectively be used to index where fastqs start in a file or string.
Next is simplified for fastq files from fasta files. Unlike fasta files, fastq always have 4 lines following each other - not variable with a line limit of 80 like fasta files have. So instead of a for loop, you can just parse 4 lines at once.
type Read ¶
type Read struct {
Identifier string `json:"identifier"`
Optionals map[string]string `json:"optionals"` // Nanopore, for example, carries along data like: `read=13956 ch=53 start_time=2020-11-11T01:49:01Z`
Sequence string `json:"sequence"`
Quality string `json:"quality"`
}
Read is a struct representing a single Fastq read element with an Identifier, its corresponding sequence, its quality score, and any optional pieces of data.
Source Files