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fq2fa.go
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fq2fa.go
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// Copyright © 2016-2019 Wei Shen <shenwei356@gmail.com>
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
// in the Software without restriction, including without limitation the rights
// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
// copies of the Software, and to permit persons to whom the Software is
// furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included in
// all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
// THE SOFTWARE.
package cmd
import (
"io"
"runtime"
"github.com/shenwei356/bio/seq"
"github.com/shenwei356/bio/seqio/fastx"
"github.com/shenwei356/xopen"
"github.com/spf13/cobra"
)
// fq2faCmd represents the fq2fa command
var fq2faCmd = &cobra.Command{
Use: "fq2fa",
Short: "convert FASTQ to FASTA",
Long: `convert FASTQ to FASTA
`,
Run: func(cmd *cobra.Command, args []string) {
config := getConfigs(cmd)
alphabet := config.Alphabet
idRegexp := config.IDRegexp
lineWidth := config.LineWidth
outFile := config.OutFile
seq.AlphabetGuessSeqLengthThreshold = config.AlphabetGuessSeqLength
seq.ValidateSeq = false
runtime.GOMAXPROCS(config.Threads)
files := getFileListFromArgsAndFile(cmd, args, true, "infile-list", true)
outfh, err := xopen.Wopen(outFile)
checkError(err)
defer outfh.Close()
var record *fastx.Record
var fastxReader *fastx.Reader
for _, file := range files {
fastxReader, err = fastx.NewReader(alphabet, file, idRegexp)
checkError(err)
for {
record, err = fastxReader.Read()
if err != nil {
if err == io.EOF {
break
}
checkError(err)
break
}
record.Seq.Qual = []byte{}
record.FormatToWriter(outfh, lineWidth)
}
}
},
}
func init() {
RootCmd.AddCommand(fq2faCmd)
}