default to not removing '*' for peptides #399

Author: shenwei356

CHANGELOG.md

@@ -8,7 +8,7 @@
     - `seqkit translate`:
         - add options `-s/--out-subseqs` and `-m/--min-len` to write ORFs longer than `x` amino acids as individual records. [#389](https://github.com/shenwei356/seqkit/issues/389)
     - `seqkit sum`:
-        - fix the logic: if `-g/--remove gaps` is not on for proteins, we'll forcely switch it on to remove possible '*'.
+        - do not remove possible '*' by default. Thanks to @photocyte. [#399](https://github.com/shenwei356/seqkit/issues/399)
         - added a progress bar for > 1 input files.
     - `seqkit pair`:
         - remove the restriction of requiring FASTQ format, i.e., FASTA files are also supported.

doc/docs/usage.md

@@ -851,10 +851,10 @@ Flags:
   -a, --all                  show all information, including the sequences length and the number of sequences
   -b, --basename             only output basename of files
   -c, --circular             the file contains a single cicular genome sequence
-  -G, --gap-letters string   gap letters (default "- \t.*")
+  -G, --gap-letters string   gap letters to delete with the flag -g/--remove-gaps (default "- \t.*")
   -h, --help                 help for sum
   -k, --kmer-size int        k-mer size for processing circular genomes (default 1000)
-  -g, --remove-gaps          remove gaps
+  -g, --remove-gaps          remove gap characters set in the option -G/gap-letters
       --rna2dna              convert RNA to DNA
   -s, --single-strand        only consider the positive strand of a circular genome, e.g., ssRNA virus
                              genomes

seqkit/cmd/sum.go

@@ -30,7 +30,6 @@ import (
 	"os"
 	"path/filepath"
 	"runtime"
-	"strings"
 	"sync"
 	"time"
 
@@ -459,13 +458,6 @@ Examples:
 							ab = fastxReader.Alphabet()
 							if ab == seq.Protein {
 								seqType = "P"
-								if !removeGaps {
-									if !strings.Contains(gapLetters, "*") {
-										gapLetters += "*"
-									}
-									removeGaps = true
-									log.Infof(`the flag -g/--remove-gaps is switched on for removing the possible stop codon '*' character for protein sequences`)
-								}
 							} else if ab == seq.RNA || ab == seq.RNAredundant {
 								seqType = "R"
 							} else if ab == seq.DNA || ab == seq.DNAredundant {
@@ -575,8 +567,8 @@ func init() {
 	sumCmd.Flags().BoolP("circular", "c", false, "the file contains a single cicular genome sequence")
 	sumCmd.Flags().IntP("kmer-size", "k", 1000, "k-mer size for processing circular genomes")
 	sumCmd.Flags().BoolP("basename", "b", false, "only output basename of files")
-	sumCmd.Flags().BoolP("remove-gaps", "g", false, "remove gaps")
-	sumCmd.Flags().StringP("gap-letters", "G", "- 	.*", "gap letters")
+	sumCmd.Flags().BoolP("remove-gaps", "g", false, "remove gap characters set in the option -G/gap-letters")
+	sumCmd.Flags().StringP("gap-letters", "G", "- 	.*", "gap letters to delete with the flag -g/--remove-gaps")
 	sumCmd.Flags().BoolP("all", "a", false, "show all information, including the sequences length and the number of sequences")
 	sumCmd.Flags().BoolP("rna2dna", "", false, "convert RNA to DNA")
 	sumCmd.Flags().BoolP("single-strand", "s", false, "only consider the positive strand of a circular genome, e.g., ssRNA virus genomes")