Created
November 1, 2023 16:48
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Go program to read and write a .gz file (fastq.gz)
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package main | |
import ( | |
"fmt" | |
// "compress/gzip" | |
gzip "github.com/klauspost/pgzip" | |
"bufio" | |
"os" | |
"log" | |
) | |
func GetReader(inputFilepath string) (*bufio.Reader, *os.File, *os.File) { | |
// defer file.Close() | |
// defer gzFile.Close() | |
var reader *bufio.Reader | |
var file *os.File | |
var gzFile *os.File | |
bufferSize := 1048576 // default 4096: 4KB ; 1048576 : 1MB ; 10485760 : 10MB | |
file, err := os.Open(inputFilepath) | |
if err != nil { | |
log.Fatalf("Error opening file: %v\n", err) | |
} | |
gz, err := gzip.NewReader(file) | |
if err != nil { | |
log.Fatalf("Error opening file: %v\n", err) | |
} | |
reader = bufio.NewReaderSize(gz, bufferSize) | |
return reader, file, gzFile | |
} | |
func GetWriter(outputFilepath string) (*os.File, *gzip.Writer) { | |
// GzWriter.Flush() | |
// GzWriter.Close() | |
// File.Close() | |
outputFile, err := os.Create(outputFilepath) | |
if err != nil { | |
log.Fatalf("Error creating output file: %v\n", err) | |
} | |
writer, err := gzip.NewWriterLevel(outputFile, gzip.BestCompression) | |
if err != nil { | |
log.Fatalf("Error creating output writer: %v\n", err) | |
} | |
return outputFile, writer | |
} | |
func main(){ | |
// input | |
inputFilepath := "data/test1.fastq.gz" | |
reader, file, gzFile := GetReader(inputFilepath) | |
defer file.Close() | |
defer gzFile.Close() | |
// output | |
outputFilepath := "data.gz" | |
outputFile, writer := GetWriter(outputFilepath) | |
defer outputFile.Close() | |
var delim byte = '\n' | |
for { | |
line, err := reader.ReadBytes(delim) // includes the delim in the output line !! | |
if err != nil { | |
break // end of file io.EOF | |
} | |
writer.Write(line) | |
} | |
writer.Flush() | |
writer.Close() | |
fmt.Println("done") | |
} |
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