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cov2simi.go
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cov2simi.go
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// Copyright © 2020-2022 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 (
"bufio"
"fmt"
"strconv"
"strings"
"github.com/spf13/cobra"
)
var cov2simiCmd = &cobra.Command{
Use: "cov2simi",
Short: "Convert k-mer coverage to sequence similarity",
Long: `Convert k-mer coverage to sequence similarity
The polynomial model of degree 3 is fitted based on simulated 150-bp E.coli reads.
Visit https://github.com/shenwei356/kmcp/tree/main/analysis/kmer-similarity
similarity = 87.456 + 26.410*qcov - 22.008*qcov*qcov + 7.325*qcov*qcov*qcov
`,
Run: func(cmd *cobra.Command, args []string) {
opt := getOptions(cmd)
var err error
outFile := getFlagString(cmd, "out-prefix")
queryCov := getFlagFloat64(cmd, "query-cov")
if queryCov < 0 || queryCov > 1 {
checkError(fmt.Errorf("value of -t/--query-cov should be in range [0, 1]"))
}
outfh, gw, w, err := outStream(outFile, strings.HasSuffix(strings.ToLower(outFile), ".gz"), opt.CompressionLevel)
checkError(err)
defer func() {
outfh.Flush()
if gw != nil {
gw.Close()
}
w.Close()
}()
if queryCov > 0 {
fmt.Fprintf(outfh, "%.6f\t%.6f\n", queryCov, similarity(queryCov))
return
}
if opt.Verbose {
log.Info("the value of flag -t/--query-cov is 0, reading from stdin/file")
}
files := getFileListFromArgsAndFile(cmd, args, true, "infile-list", true)
if opt.Verbose {
if len(files) == 1 && isStdin(files[0]) {
log.Info("no files given, reading from stdin")
} else {
log.Infof("%d input file(s) given", len(files))
}
}
var line string
var qcov float64
for _, file := range files {
infh, r, _, err := inStream(file)
checkError(err)
scanner := bufio.NewScanner(infh)
for scanner.Scan() {
line = scanner.Text()
if line == "" {
continue
}
qcov, err = strconv.ParseFloat(line, 64)
if err != nil {
checkError(fmt.Errorf("input should be a number: %s", line))
}
fmt.Fprintf(outfh, "%s\t%.6f\n", line, similarity(qcov))
}
if err := scanner.Err(); err != nil {
checkError(err)
}
r.Close()
}
},
}
func init() {
utilsCmd.AddCommand(cov2simiCmd)
cov2simiCmd.Flags().StringP("out-prefix", "o", "-", formatFlagUsage(`Out file prefix ("-" for stdout).`))
cov2simiCmd.Flags().Float64P("query-cov", "t", 0,
formatFlagUsage(`K-mer query coverage, i.e., proportion of matched k-mers and unique k-mers of a query. range: [0, 1]`))
}