unikmer locate/uniqs: fix option checking

shenwei356 · Nov 7, 2018 · 1e23909 · 1e23909
1 parent 947d2c4
commit 1e23909
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Showing 17 changed files with 32 additions and 18 deletions.
diff --git a/CHANGES.md b/CHANGES.md
@@ -1,3 +1,5 @@
+- v0.5.1
+    - `unikmer locate/uniqs`: fix options checking
 - v0.5.0
     - `unikmer diff`: fix concurrency bug when cloning kmers from first file.
     - new command `unikmer locate`: locate Kmers in genome.

diff --git a/unikmer/cmd/concat.go b/unikmer/cmd/concat.go
@@ -56,7 +56,7 @@ Attentions:
 			files = getFileList(args)
 		}
 
-		checkFiles(files)
+		checkFiles(extDataFile, files...)
 
 		outFile := getFlagString(cmd, "out-prefix")
 

diff --git a/unikmer/cmd/diff.go b/unikmer/cmd/diff.go
@@ -61,7 +61,7 @@ Tips:
 			files = getFileList(args)
 		}
 
-		checkFiles(files)
+		checkFiles(extDataFile, files...)
 
 		outFile := getFlagString(cmd, "out-prefix")
 		sortKmers := getFlagBool(cmd, "sort")

diff --git a/unikmer/cmd/grep.go b/unikmer/cmd/grep.go
@@ -60,7 +60,7 @@ var grepCmd = &cobra.Command{
 			checkError(fmt.Errorf("no more than one file should be given"))
 		}
 
-		checkFiles(files)
+		checkFiles(extDataFile, files...)
 
 		outFile := getFlagString(cmd, "out-file")
 		pattern := getFlagStringSlice(cmd, "query")

diff --git a/unikmer/cmd/inter.go b/unikmer/cmd/inter.go
@@ -54,7 +54,7 @@ var interCmd = &cobra.Command{
 			files = getFileList(args)
 		}
 
-		checkFiles(files)
+		checkFiles(extDataFile, files...)
 
 		outFile := getFlagString(cmd, "out-prefix")
 		sortKmers := getFlagBool(cmd, "sort")

diff --git a/unikmer/cmd/locate.go b/unikmer/cmd/locate.go
@@ -60,15 +60,16 @@ Attention:
 			files = getFileList(args)
 		}
 
-		checkFiles(files)
+		checkFiles(extDataFile, files...)
 		if len(files) == 1 && isStdin(files[0]) {
 			checkError(fmt.Errorf("stdin not supported, please give me .unik files"))
 		}
 
 		outFile := getFlagString(cmd, "out-prefix")
 		circular := getFlagBool(cmd, "circular")
 
-		genomeFile := getFlagString(cmd, "genome")
+		genomeFile := getFlagNonEmptyString(cmd, "genome")
+		checkFiles("", genomeFile)
 
 		// -----------------------------------------------------------------------
 

diff --git a/unikmer/cmd/num.go b/unikmer/cmd/num.go
@@ -53,7 +53,7 @@ var numCmd = &cobra.Command{
 			files = getFileList(args)
 		}
 
-		checkFiles(files)
+		checkFiles(extDataFile, files...)
 
 		outFile := getFlagString(cmd, "out-file")
 		showFile := getFlagBool(cmd, "file-name")

diff --git a/unikmer/cmd/sample.go b/unikmer/cmd/sample.go
@@ -58,7 +58,7 @@ Attentions:
 			files = getFileList(args)
 		}
 
-		checkFiles(files)
+		checkFiles(extDataFile, files...)
 
 		outFile := getFlagString(cmd, "out-prefix")
 

diff --git a/unikmer/cmd/sort.go b/unikmer/cmd/sort.go
@@ -53,7 +53,7 @@ var sortCmd = &cobra.Command{
 			files = getFileList(args)
 		}
 
-		checkFiles(files)
+		checkFiles(extDataFile, files...)
 
 		outFile := getFlagString(cmd, "out-prefix")
 		unique := getFlagBool(cmd, "unique")

diff --git a/unikmer/cmd/stats.go b/unikmer/cmd/stats.go
@@ -63,7 +63,7 @@ Tips:
 			files = getFileList(args)
 		}
 
-		checkFiles(files)
+		checkFiles(extDataFile, files...)
 
 		outFile := getFlagString(cmd, "out-file")
 		all := getFlagBool(cmd, "all")

diff --git a/unikmer/cmd/subset.go b/unikmer/cmd/subset.go
@@ -62,7 +62,7 @@ Attention:
 			checkError(fmt.Errorf("no more than one file should be given"))
 		}
 
-		checkFiles(files)
+		checkFiles(extDataFile, files...)
 
 		outFile := getFlagString(cmd, "out-prefix")
 		k := getFlagPositiveInt(cmd, "kmer-len")

diff --git a/unikmer/cmd/union.go b/unikmer/cmd/union.go
@@ -58,7 +58,7 @@ Attentions:
 			files = getFileList(args)
 		}
 
-		checkFiles(files)
+		checkFiles(extDataFile, files...)
 
 		outFile := getFlagString(cmd, "out-prefix")
 		sortKmers := getFlagBool(cmd, "sort")

diff --git a/unikmer/cmd/uniqs.go b/unikmer/cmd/uniqs.go
@@ -60,12 +60,14 @@ Attention:
 			files = getFileList(args)
 		}
 
-		checkFiles(files)
+		checkFiles(extDataFile, files...)
 
 		outFile := getFlagString(cmd, "out-prefix")
 		circular := getFlagBool(cmd, "circular")
 
-		genomeFile := getFlagString(cmd, "genome")
+		genomeFile := getFlagNonEmptyString(cmd, "genome")
+		checkFiles("", genomeFile)
+
 		minLen := getFlagPositiveInt(cmd, "min-len")
 		mMapped := getFlagBool(cmd, "allow-muliple-mapped-kmer")
 		outputFASTA := getFlagBool(cmd, "output-fasta")

diff --git a/unikmer/cmd/util-cli.go b/unikmer/cmd/util-cli.go
@@ -120,6 +120,15 @@ func getFlagString(cmd *cobra.Command, flag string) string {
 	return value
 }
 
+func getFlagNonEmptyString(cmd *cobra.Command, flag string) string {
+	value, err := cmd.Flags().GetString(flag)
+	checkError(err)
+	if value == "" {
+		checkError(fmt.Errorf("flag --%s needed", flag))
+	}
+	return value
+}
+
 func getFlagCommaSeparatedStrings(cmd *cobra.Command, flag string) []string {
 	value, err := cmd.Flags().GetString(flag)
 	checkError(err)

diff --git a/unikmer/cmd/util.go b/unikmer/cmd/util.go
@@ -138,7 +138,7 @@ func extendDegenerateSeq(s []byte) (dseqs [][]byte, err error) {
 	return dseqs, nil
 }
 
-func checkFiles(files []string) {
+func checkFiles(suffix string, files ...string) {
 	for _, file := range files {
 		if isStdin(file) {
 			continue
@@ -150,7 +150,7 @@ func checkFiles(files []string) {
 		if !ok {
 			checkError(fmt.Errorf("file (linked file) does not exist: %s", file))
 		}
-		if !strings.HasSuffix(file, extDataFile) {
+		if suffix != "" && !strings.HasSuffix(file, suffix) {
 			checkError(fmt.Errorf("input should be stdin or %s file: %s", extDataFile, file))
 		}
 	}

diff --git a/unikmer/cmd/version.go b/unikmer/cmd/version.go
@@ -29,7 +29,7 @@ import (
 )
 
 // VERSION is the version
-var VERSION = "0.5.0"
+var VERSION = "0.5.1"
 
 // versionCmd represents the version command
 var versionCmd = &cobra.Command{

diff --git a/unikmer/cmd/view.go b/unikmer/cmd/view.go
@@ -54,7 +54,7 @@ var viewCmd = &cobra.Command{
 			files = getFileList(args)
 		}
 
-		checkFiles(files)
+		checkFiles(extDataFile, files...)
 
 		outFile := getFlagString(cmd, "out-file")
 		showCode := getFlagBool(cmd, "show-code")