reformat: add a new placeholder "{K}" for rank "kingdom". #64

shenwei356 · Aug 25, 2022 · a73772d · a73772d
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,6 @@
 - [TaxonKit v0.12.1](https://github.com/shenwei356/taxonkit/releases/tag/v0.12.1)
 [![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.12.1/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.12.1)
+    - `taxonkit reformat`: add a new placeholder `{K}` for rank `kingdom`. [#64](https://github.com/shenwei356/taxonkit/issues/64)
     - `taxonkit create-taxdump`: 
         - fix merged.dmp and delnodes.dmp. [gtdb-taxdump/issues/2](https://github.com/shenwei356/gtdb-taxdump/issues/2)
         - fix bug of handling non-GTDB data when using `-A/--field-accession` and no rank names given.

diff --git a/taxonkit/cmd/reformat.go b/taxonkit/cmd/reformat.go
@@ -62,6 +62,7 @@ Ambiguous names:
 Output format can be formated by flag --format, available placeholders:
 
     {k}: superkingdom
+    {K}: kingdom
     {p}: phylum
     {c}: class
     {o}: order
@@ -114,6 +115,7 @@ Output format can contains some escape charactors like "\t".
 
 		addPrefix := getFlagBool(cmd, "add-prefix")
 		prefixK := getFlagString(cmd, "prefix-k")
+		prefixK2 := getFlagString(cmd, "prefix-K")
 		prefixP := getFlagString(cmd, "prefix-p")
 		prefixC := getFlagString(cmd, "prefix-c")
 		prefixO := getFlagString(cmd, "prefix-o")
@@ -128,6 +130,7 @@ Output format can contains some escape charactors like "\t".
 
 		prefixes := map[string]string{
 			"k": prefixK,
+			"K": prefixK2,
 			"p": prefixP,
 			"c": prefixC,
 			"o": prefixO,
@@ -516,6 +519,7 @@ func init() {
 
 	flineageCmd.Flags().BoolP("add-prefix", "P", false, `add prefixes for all ranks, single prefix for a rank is defined by flag --prefix-X`)
 	flineageCmd.Flags().StringP("prefix-k", "", "k__", `prefix for superkingdom, used along with flag -P/--add-prefix`)
+	flineageCmd.Flags().StringP("prefix-K", "", "K__", `prefix for kingdom, used along with flag -P/--add-prefix`)
 	flineageCmd.Flags().StringP("prefix-p", "", "p__", `prefix for phylum, used along with flag -P/--add-prefix`)
 	flineageCmd.Flags().StringP("prefix-c", "", "c__", `prefix for class, used along with flag -P/--add-prefix`)
 	flineageCmd.Flags().StringP("prefix-o", "", "o__", `prefix for order, used along with flag -P/--add-prefix`)

diff --git a/taxonkit/cmd/util-rank.go b/taxonkit/cmd/util-rank.go
@@ -25,6 +25,7 @@ import "regexp"
 var rankList = []string{
 	"",
 	"superkingdom",
+	"kingdom",
 	"phylum",
 	"class",
 	"order",
@@ -39,6 +40,7 @@ var rankList = []string{
 var srankList = []string{
 	"",
 	"k",
+	"K",
 	"p",
 	"c",
 	"o",
@@ -52,6 +54,7 @@ var srankList = []string{
 
 var rank2symbol = map[string]string{
 	"superkingdom":      "k",
+	"kingdom":           "K",
 	"phylum":            "p",
 	"class":             "c",
 	"order":             "o",
@@ -65,6 +68,7 @@ var rank2symbol = map[string]string{
 
 var symbol2rank = map[string]string{
 	"k": "superkingdom",
+	"K": "kingdom",
 	"p": "phylum",
 	"c": "class",
 	"o": "order",
@@ -77,6 +81,7 @@ var symbol2rank = map[string]string{
 }
 var symbol2weight = map[string]float32{
 	"k": 1,
+	"K": 1.5,
 	"p": 2,
 	"c": 3,
 	"o": 4,
@@ -92,6 +97,7 @@ var reRankPlaceHolder = regexp.MustCompile(`\{(\w)\}`)
 
 var reRankPlaceHolders = map[string]*regexp.Regexp{
 	"k": regexp.MustCompile(`\{k\}`),
+	"K": regexp.MustCompile(`\{K\}`),
 	"p": regexp.MustCompile(`\{p\}`),
 	"c": regexp.MustCompile(`\{c\}`),
 	"o": regexp.MustCompile(`\{o\}`),