v0.3.4

README.md

@@ -10,19 +10,22 @@ Latest version: [![Latest Version](https://img.shields.io/github/release/shenwei
 
 ## Introduction
 
-FASTA and FASTQ are basic formats for storing nucleotide and protein sequences.
-The manipulations of FASTA/Q file include converting, clipping, searching,
-filtering, deduplication, splitting, shuffling, sampling and so on.
-Existed tools only implemented parts of the functions,
-and some of them are only available for specific operating systems.
-Furthermore, the complicated installation process of dependencies packages and
-running environment also make them less friendly to common users.
-
-SeqKit is a cross-platform, ultrafast, and practical FASTA/Q manipulations tool
-that is friendly for researchers to complete wide ranges of FASTA/Q file processing.
-The toolkit supports plain or gzip-compressed input and output
-from either standard stream or files,
-therefore, it could be easily used in command-line pipe.
+FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and
+protein sequences. Common manipulations of FASTA/Q file include converting,
+searching, filtering, deduplication, splitting, shuffling, and sampling.
+Existing tools only implement some of these manipulations,
+and not particularly efficiently, and some are only available for certain
+operating systems. Furthermore, the complicated installation process of
+required packages and running environments can render these programs less
+user friendly.
+
+This project describes a cross-platform ultrafast comprehensive
+toolkit for FASTA/Q processing. SeqKit provides executable binary files for
+all major operating systems, including Windows, Linux, and Mac OS X, and can
+be directly used without any dependencies or pre-configurations.
+SeqKit demonstrates competitive performance in execution time and memory
+usage compared to similar tools. The efficiency and usability of SeqKit
+enable researchers to rapidly accomplish common FASTA/Q file manipulations.
 
 ## Features
 
@@ -203,7 +206,7 @@ when input files are (plain or gzipped) FASTA files,
 FASTA index would be optional used for
 rapid access of sequences and reducing memory occupation.
 
-ATTENTION: the `.seqkit.fai` file created by SeqKit is a little different from `.fai` file
+ATTENTION: the `.seqkit.fai` file created by SeqKit is slightly different from `.fai` file
 created by `samtools`. SeqKit uses full sequence head instead of just ID as key.
 
 ### Parallelization of CPU intensive jobs

doc/docs/download.md

@@ -6,8 +6,10 @@ SeqKit is implemented in [Golang](https://golang.org/) programming language,
 
 ## Latest Version
 
-[SeqKit v0.3.3](https://github.com/shenwei356/seqkit/releases/tag/v0.3.3)
-
+[SeqKit v0.3.4](https://github.com/shenwei356/seqkit/releases/tag/v0.3.3)
+- new feature: `fxtab` could output alphabet letters of a sequence
+- new feature: new flag `-K` (`--keep-key`) for `replace`,  when replacing
+with key-value file, one can choose keeping the key as value or not.
 
 ***64-bit versions are highly recommended.***
 
@@ -76,7 +78,8 @@ For Go developer, just one command:
     go get -u github.com/shenwei356/seqkit/seqkit
 
 ## Release History
-
+- [SeqKit v0.3.3](https://github.com/shenwei356/seqkit/releases/tag/v0.3.4)
+    - add feature: `seqkit fx2tab ` can print the alphabet letters of every sequence with flag `-a` (`--alphabet`)
 - [SeqKit v0.3.3](https://github.com/shenwei356/seqkit/releases/tag/v0.3.3)
     - fix bug of `seqkit replace`, wrongly starting from 2 when using `{nr}`
       in `-r` (`--replacement`)

doc/docs/usage.md

@@ -1038,7 +1038,7 @@ Or use the \ escape character.
 
 more on: http://bioinf.shenwei.me/seqkit/usage/#replace
 
-Special repalcement symbols:
+Special replacement symbols (only for replacing name not sequence):
 
         {nr}    Record number, starting from 1
         {kv}    Corresponding value of the key ($1) by key-value file
@@ -1048,7 +1048,8 @@ Usage:
 
 Flags:
   -s, --by-seq               replace seq
-  -i, --ignore-case          ignore case
+  -i, --ignore-case          ignore case  
+  -K, --keep-key             keep the key as value when no value found for the key
   -k, --kv-file string       tab-delimited key-value file for replacing key with value when using "{kv}" in -r (--replacement)
   -p, --pattern string       search regular expression
   -r, --replacement string   replacement. supporting capture variables.  e.g. $1 represents the text of the first submatch. ATTENTION: use SINGLE quote NOT double quotes in *nix OS or use the \ escape character. Record number is also supported by "{nr}"
@@ -1095,12 +1096,13 @@ Examples
 
 1. Rename with number of record
 
-        echo -e ">abc\nACTG\n>123\nATTT" |  seqkit replace -p .+ -r "seq_{NR}"
+        echo -e ">abc\nACTG\n>123\nATTT" |  seqkit replace -p .+ -r "seq_{nr}"
         >seq_1
         ACTG
         >seq_2
         ATTT
 
+1. Replace key
 
 ## shuffle
 

seqkit/cmd/fx2tab.go

@@ -24,10 +24,12 @@ import (
 	"fmt"
 	"io"
 	"runtime"
+	"sort"
+	"strings"
 
-	"github.com/shenwei356/xopen"
 	"github.com/shenwei356/bio/seq"
 	"github.com/shenwei356/bio/seqio/fastx"
+	"github.com/shenwei356/xopen"
 	"github.com/spf13/cobra"
 )
 
@@ -57,6 +59,7 @@ like sequence length, GC content/GC skew.
 		baseContents := getFlagStringSlice(cmd, "base-content")
 		onlyName := getFlagBool(cmd, "name")
 		printTitle := getFlagBool(cmd, "header-line")
+		printAlphabet := getFlagBool(cmd, "alphabet")
 
 		outfh, err := xopen.Wopen(outFile)
 		checkError(err)
@@ -78,6 +81,10 @@ like sequence length, GC content/GC skew.
 					outfh.WriteString(fmt.Sprintf("\t%s", bc))
 				}
 			}
+			if printAlphabet {
+				outfh.WriteString("\talphabet")
+			}
+
 			outfh.WriteString("\n")
 		}
 
@@ -132,6 +139,10 @@ like sequence length, GC content/GC skew.
 						outfh.WriteString(fmt.Sprintf("\t%.2f", record.Seq.BaseContent(bc)*100))
 					}
 				}
+
+				if printAlphabet {
+					outfh.WriteString(fmt.Sprintf("\t%s", alphabetStr(record.Seq.Seq)))
+				}
 				outfh.WriteString("\n")
 			}
 		}
@@ -148,4 +159,20 @@ func init() {
 	fx2tabCmd.Flags().BoolP("only-id", "i", false, "print ID instead of full head")
 	fx2tabCmd.Flags().BoolP("name", "n", false, "only print names (no sequences and qualities)")
 	fx2tabCmd.Flags().BoolP("header-line", "H", false, "print header line")
+	fx2tabCmd.Flags().BoolP("alphabet", "a", false, "print alphabet letters")
+}
+
+func alphabetStr(s []byte) string {
+	m := make(map[byte]struct{})
+	for _, b := range s {
+		m[b] = struct{}{}
+	}
+	alphabet := make([]string, len(m))
+	i := 0
+	for a := range m {
+		alphabet[i] = string([]byte{a})
+		i++
+	}
+	sort.Strings(alphabet)
+	return strings.Join(alphabet, "")
 }

seqkit/cmd/helper.go

@@ -43,7 +43,7 @@ import (
 )
 
 // VERSION of seqkit
-const VERSION = "0.3.3"
+const VERSION = "0.3.4"
 
 func checkError(err error) {
 	if err != nil {

seqkit/cmd/replace.go

@@ -54,7 +54,7 @@ Or use the \ escape character.
 
 more on: http://bioinf.shenwei.me/seqkit/usage/#replace
 
-Special repalcement symbols:
+Special replacement symbols (only for replacing name not sequence):
 
 	{nr}	Record number, starting from 1
 	{kv}	Corresponding value of the key ($1) by key-value file
@@ -73,6 +73,7 @@ Special repalcement symbols:
 		pattern := getFlagString(cmd, "pattern")
 		replacement := []byte(getFlagString(cmd, "replacement"))
 		kvFile := getFlagString(cmd, "kv-file")
+		keepKey := getFlagBool(cmd, "keep-key")
 
 		bySeq := getFlagBool(cmd, "by-seq")
 		// byName := getFlagBool(cmd, "by-name")
@@ -100,6 +101,9 @@ Special repalcement symbols:
 			if !regexp.MustCompile(`\(.+\)`).MatchString(pattern) {
 				checkError(fmt.Errorf(`value of -p (--pattern) must contains "(" and ")" to capture data which is used specify the KEY`))
 			}
+			if bySeq {
+				checkError(fmt.Errorf(`replaceing with key-value pairs was not supported for sequence`))
+			}
 			if kvFile == "" {
 				checkError(fmt.Errorf(`since repalcement symbol "{kv}"/"{KV}" found in value of flag -r (--replacement), tab-delimited key-value file should be given by flag -k (--kv-file)`))
 			}
@@ -167,8 +171,10 @@ Special repalcement symbols:
 							}
 							if _, ok = kvs[k]; ok {
 								r = reKV.ReplaceAll(r, []byte(kvs[k]))
-							} else {
+							} else if keepKey {
 								r = reKV.ReplaceAll(r, found[1])
+							} else {
+								r = reKV.ReplaceAll(r, []byte(""))
 							}
 						}
 					}
@@ -196,6 +202,7 @@ func init() {
 	replaceCmd.Flags().BoolP("ignore-case", "i", false, "ignore case")
 	replaceCmd.Flags().StringP("kv-file", "k", "",
 		`tab-delimited key-value file for replacing key with value when using "{kv}" in -r (--replacement)`)
+	replaceCmd.Flags().BoolP("keep-key", "K", false, "keep the key as value when no value found for the key")
 }
 
 var reNR = regexp.MustCompile(`\{(NR|nr)\}`)

seqkit/download_all_binaries.sh

@@ -1,7 +1,7 @@
 #!/bin/sh
 
 rm seqkit_*.tar.gz
-version="0.3.2"
+version="0.3.4"
 
 wget https://github.com/shenwei356/seqkit/releases/download/v$version/seqkit_linux_386.tar.gz
 wget https://github.com/shenwei356/seqkit/releases/download/v$version/seqkit_linux_amd64.tar.gz