Accept input TaxIds from stdin/files. #93

shenwei356 · Jun 15, 2024 · 552e9ee · 552e9ee
1 parent 668d610
commit 552e9ee
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Showing 4 changed files with 55 additions and 6 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,7 +1,9 @@
-- [TaxonKit v0.16.1](https://github.com/shenwei356/taxonkit/releases/tag/v0.16.1)
-[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.16.1/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.16.1)
+- [TaxonKit v0.17.0](https://github.com/shenwei356/taxonkit/releases/tag/v0.17.0)
+[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.17.0/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.17.0)
     - `taxonkit filter`:
         - Fix keeping taxids with a rank of "no rank" or "clade". [#97](https://github.com/shenwei356/taxonkit/issues/97)
+    - `taxonkit list`:
+        - Accept input TaxIds from stdin/files, not just the flag `--ids`. [#93](https://github.com/shenwei356/taxonkit/issues/93)
 - [TaxonKit v0.16.0](https://github.com/shenwei356/taxonkit/releases/tag/v0.16.0)
 [![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.16.0/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.16.0)
     - `taxonkit create-taxdump`:

diff --git a/taxonkit/cmd/list.go b/taxonkit/cmd/list.go
@@ -54,6 +54,12 @@ Examples:
     63221
     741158
 
+    # from stdin
+    echo 9606 | taxonkit list
+
+    # from file
+    taxonkit list <(echo 9606)
+
 `,
 	Run: func(cmd *cobra.Command, args []string) {
 		config := getConfigs(cmd)
@@ -63,10 +69,17 @@ Examples:
 		jsonFormat := getFlagBool(cmd, "json")
 
 		files := getFileList(args)
-		if len(files) > 1 || (len(files) == 1 && files[0] == "stdin") {
-			log.Warningf("no positional arguments needed")
+		// if len(files) > 1 || (len(files) == 1 && files[0] == "stdin") {
+		// 	log.Warningf("no positional arguments needed")
+		// }
+
+		if len(ids) == 0 && len(files) == 1 && isStdin(files[0]) && !xopen.IsStdin() {
+			checkError(fmt.Errorf("stdin not detected"))
 		}
 
+		_ids := getTaxonIDs(files)
+		ids = append(ids, _ids...)
+
 		outfh, err := xopen.Wopen(config.OutFile)
 		checkError(err)
 		defer outfh.Close()

diff --git a/taxonkit/cmd/util-cli.go b/taxonkit/cmd/util-cli.go
@@ -21,6 +21,7 @@
 package cmd
 
 import (
+	"bufio"
 	"fmt"
 	"os"
 	"path/filepath"
@@ -31,6 +32,7 @@ import (
 
 	"github.com/pkg/errors"
 	"github.com/shenwei356/util/pathutil"
+	"github.com/shenwei356/xopen"
 	"github.com/spf13/cobra"
 	"github.com/twotwotwo/sorts"
 )
@@ -127,7 +129,8 @@ func getFlagTaxonIDs(cmd *cobra.Command, flag string) []int {
 	s, err := cmd.Flags().GetString(flag)
 	checkError(err)
 	if s == "" {
-		checkError(fmt.Errorf("flag --%s needed", flag))
+		// checkError(fmt.Errorf("flag --%s needed", flag))
+		return nil
 	}
 	if !reTaxIDs.MatchString(s) {
 		checkError(fmt.Errorf("invalid value of flag %s. comma-separated integers needed", flag))
@@ -142,6 +145,37 @@ func getFlagTaxonIDs(cmd *cobra.Command, flag string) []int {
 	return ids
 }
 
+func getTaxonIDs(files []string) []int {
+	ids := make([]int, 0, 1024)
+	var id int
+	var line string
+	for _, file := range files {
+		fh, err := xopen.Ropen(file)
+		checkError(err)
+
+		scanner := bufio.NewScanner(fh)
+		for scanner.Scan() {
+			line = strings.Trim(scanner.Text(), "\t\r\n")
+			if line == "" {
+				continue
+			}
+			id, err = strconv.Atoi(line)
+			if err != nil {
+				continue
+			}
+
+			ids = append(ids, id)
+		}
+		if err := scanner.Err(); err != nil {
+			checkError(err)
+		}
+
+		checkError(fh.Close())
+	}
+
+	return ids
+}
+
 func makeOutDir(outDir string, force bool) {
 	pwd, _ := os.Getwd()
 	if outDir != "./" && outDir != "." && pwd != filepath.Clean(outDir) {

diff --git a/taxonkit/cmd/version.go b/taxonkit/cmd/version.go
@@ -29,7 +29,7 @@ import (
 )
 
 // VERSION of taxonkit
-const VERSION = "0.16.0"
+const VERSION = "0.17.0"
 
 // versionCmd represents the version command
 var versionCmd = &cobra.Command{