add the --skip-empty option

Former-commit-id: ec9cb0ecaf90a61bf9289cf4c089b5cc2fcb65a5

Release-notes.md

@@ -4,7 +4,9 @@
 
 ### Bugs
 
-- Patch a bug in the install script for correctly follow download redirection.
+- Patch a bug in the install-script for correctly follow download redirection.
+- Patch a bug in `obitagpcr` to consider the renaming of the `forward_mismatch` and `reverse_mismatch` tags
+  to `forward_error` and `reverse_error`.
 
 ### Enhancement
 
@@ -14,6 +16,10 @@
 
 ### New feature
 
+- In every *OBITools*, writing an empty sequence (sequence of length equal to zero) through an error and
+  stops the execution of the tool, except if the **--skip-empty** option is set. In that case, the empty
+  sequence is ignored and not printed to the output. When output involved paired sequence the **--skip-empty** 
+  option is ignored. 
 - In `obiannotate` adds the **--set-identifier** option to edit the sequence identifier
 - In `obitag` adds the **--save-db** option allowing at the end of the run of `obitag` to save a
   modified version of the reference database containing the computed index. This allows next

cmd/obitools/obiclean/main.go

@@ -2,6 +2,7 @@ package main
 
 import (
 	"os"
+
 	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
@@ -19,11 +20,11 @@ func main() {
 	fs, err := obiconvert.CLIReadBioSequences(args...)
 
 	if err != nil {
-		log.Errorf("Cannot open file (%v)",err)
+		log.Errorf("Cannot open file (%v)", err)
 		os.Exit(1)
 	}
 
-	cleaned := obiclean.IOBIClean(fs)
+	cleaned := obiclean.CLIOBIClean(fs)
 
 	obiconvert.CLIWriteBioSequences(cleaned, true)
 

go.mod

@@ -19,6 +19,7 @@ require (
 )
 
 require (
+	github.com/chen3feng/stl4go v0.1.1 // indirect
 	github.com/klauspost/compress v1.16.3 // indirect
 	github.com/mattn/go-runewidth v0.0.14 // indirect
 	github.com/mitchellh/colorstring v0.0.0-20190213212951-d06e56a500db // indirect

go.sum

@@ -6,6 +6,8 @@ github.com/PaesslerAG/jsonpath v0.1.0 h1:gADYeifvlqK3R3i2cR5B4DGgxLXIPb3TRTH1mGi
 github.com/PaesslerAG/jsonpath v0.1.0/go.mod h1:4BzmtoM/PI8fPO4aQGIusjGxGir2BzcV0grWtFzq1Y8=
 github.com/barkimedes/go-deepcopy v0.0.0-20220514131651-17c30cfc62df h1:GSoSVRLoBaFpOOds6QyY1L8AX7uoY+Ln3BHc22W40X0=
 github.com/barkimedes/go-deepcopy v0.0.0-20220514131651-17c30cfc62df/go.mod h1:hiVxq5OP2bUGBRNS3Z/bt/reCLFNbdcST6gISi1fiOM=
+github.com/chen3feng/stl4go v0.1.1 h1:0L1+mDw7pomftKDruM23f1mA7miavOj6C6MZeadzN2Q=
+github.com/chen3feng/stl4go v0.1.1/go.mod h1:5ml3psLgETJjRJnMbPE+JiHLrCpt+Ajc2weeTECXzWU=
 github.com/daichi-m/go18ds v1.12.1 h1:Pjc3IApmN4qtDiovGP9MvMpIzgZle3SHUcNaA5j46bg=
 github.com/daichi-m/go18ds v1.12.1/go.mod h1:wc2dURUr8aMxxC4Mn5ObJGVM7uIKU8JagY4nhtonXq8=
 github.com/davecgh/go-spew v1.1.0/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=

pkg/obiformats/fastseq_write_fasta.go

@@ -55,11 +55,19 @@ func FormatFasta(seq *obiseq.BioSequence, formater FormatHeader) string {
 		folded)
 }
 
-func FormatFastaBatch(batch obiiter.BioSequenceBatch, formater FormatHeader) []byte {
+func FormatFastaBatch(batch obiiter.BioSequenceBatch, formater FormatHeader, skipEmpty bool) []byte {
 	var bs bytes.Buffer
 	for _, seq := range batch.Slice() {
-		bs.WriteString(FormatFasta(seq, formater))
-		bs.WriteString("\n")
+		if seq.Len() > 0 {
+			bs.WriteString(FormatFasta(seq, formater))
+			bs.WriteString("\n")	
+		} else {
+			if skipEmpty {
+				log.Warnf("Sequence %s is empty and skiped in output",seq.Id())
+			} else {
+				log.Fatalf("Sequence %s is empty",seq.Id())
+			}
+		}
 	}
 	return bs.Bytes()
 }
@@ -99,7 +107,7 @@ func WriteFasta(iterator obiiter.IBioSequence,
 			batch := iterator.Get()
 
 			chunkchan <- FileChunck{
-				FormatFastaBatch(batch, header_format),
+				FormatFastaBatch(batch, header_format, opt.SkipEmptySequence()),
 				batch.Order(),
 			}
 			newIter.Push(batch)

pkg/obiformats/fastseq_write_fastq.go

@@ -39,11 +39,20 @@ func FormatFastq(seq *obiseq.BioSequence, quality_shift int, formater FormatHead
 }
 
 func FormatFastqBatch(batch obiiter.BioSequenceBatch, quality_shift int,
-	formater FormatHeader) []byte {
+	formater FormatHeader, skipEmpty bool) []byte {
 	var bs bytes.Buffer
 	for _, seq := range batch.Slice() {
-		bs.WriteString(FormatFastq(seq, quality_shift, formater))
-		bs.WriteString("\n")
+		if seq.Len() > 0 {
+			bs.WriteString(FormatFastq(seq, quality_shift, formater))
+			bs.WriteString("\n")
+		} else {
+			if skipEmpty {
+				log.Warnf("Sequence %s is empty and skiped in output", seq.Id())
+			} else {
+				log.Fatalf("Sequence %s is empty", seq.Id())
+			}
+		}
+
 	}
 	return bs.Bytes()
 }
@@ -90,7 +99,7 @@ func WriteFastq(iterator obiiter.IBioSequence,
 		for iterator.Next() {
 			batch := iterator.Get()
 			chunk := FileChunck{
-				FormatFastqBatch(batch, quality, header_format),
+				FormatFastqBatch(batch, quality, header_format, opt.SkipEmptySequence()),
 				batch.Order(),
 			}
 			chunkchan <- chunk

pkg/obiformats/options.go

@@ -16,6 +16,7 @@ type __options__ struct {
 	closefile             bool
 	appendfile            bool
 	compressed            bool
+	skip_empty            bool
 	csv_id                bool
 	csv_sequence          bool
 	csv_quality           bool
@@ -48,6 +49,7 @@ func MakeOptions(setters []WithOption) Options {
 		closefile:             false,
 		appendfile:            false,
 		compressed:            false,
+		skip_empty:            false,
 		csv_id:                true,
 		csv_definition:        false,
 		csv_count:             false,
@@ -110,6 +112,10 @@ func (opt Options) CompressedFile() bool {
 	return opt.pointer.compressed
 }
 
+func (opt Options) SkipEmptySequence() bool {
+	return opt.pointer.skip_empty
+}
+
 func (opt Options) CSVId() bool {
 	return opt.pointer.csv_id
 }
@@ -194,6 +200,14 @@ func OptionsCompressed(compressed bool) WithOption {
 	return f
 }
 
+func OptionsSkipEmptySequence(skip bool) WithOption {
+	f := WithOption(func(opt Options) {
+		opt.pointer.skip_empty = skip
+	})
+
+	return f
+}
+
 func OptionsNewFile() WithOption {
 	f := WithOption(func(opt Options) {
 		opt.pointer.appendfile = false

pkg/obitools/obiclean/obiclean.go

@@ -285,7 +285,7 @@ func Weight(sequence *obiseq.BioSequence) map[string]int {
 	return weight
 }
 
-func IOBIClean(itertator obiiter.IBioSequence) obiiter.IBioSequence {
+func CLIOBIClean(itertator obiiter.IBioSequence) obiiter.IBioSequence {
 
 	db := itertator.Load()
 

pkg/obitools/obiconvert/options.go

@@ -26,6 +26,7 @@ var __output_solexa_quality__ = false
 
 var __no_progress_bar__ = false
 var __compressed__ = false
+var __skip_empty__ = false
 
 var __output_file_name__ = "-"
 var __paired_file_name__ = ""
@@ -70,6 +71,9 @@ func OutputModeOptionSet(options *getoptions.GetOpt) {
 		options.Alias("Z"),
 		options.Description("Output is compressed"))
 
+		options.BoolVar(&__skip_empty__, "skip-empty", __skip_empty__,
+		options.Description("Sequences of length equal to zero are suppressed from the output"))
+
 	options.StringVar(&__output_file_name__, "out", __output_file_name__,
 		options.Alias("o"),
 		options.ArgName("FILENAME"),
@@ -141,6 +145,10 @@ func CLICompressed() bool {
 	return __compressed__
 }
 
+func CLISkipEmpty() bool {
+	return __skip_empty__ 
+}
+
 func CLIInputFastHeaderFormat() string {
 	switch {
 	case __input_fastjson_format__:

pkg/obitools/obiconvert/sequence_writer.go

@@ -80,6 +80,8 @@ func CLIWriteBioSequences(iterator obiiter.IBioSequence,
 			var reverse string
 			fn, reverse = BuildPairedFileNames(fn)
 			opts = append(opts, obiformats.WritePairedReadsTo(reverse))
+		} else {
+			opts = append(opts, obiformats.OptionsSkipEmptySequence(CLISkipEmpty()))
 		}
 
 		switch CLIOutputFormat() {
@@ -91,6 +93,7 @@ func CLIWriteBioSequences(iterator obiiter.IBioSequence,
 			newIter, err = obiformats.WriteSequencesToFile(iterator, fn, opts...)
 		}
 	} else {
+		opts = append(opts, obiformats.OptionsSkipEmptySequence(CLISkipEmpty()))
 		switch CLIOutputFormat() {
 		case "fastq":
 			newIter, err = obiformats.WriteFastqToStdout(iterator, opts...)
@@ -99,6 +102,7 @@ func CLIWriteBioSequences(iterator obiiter.IBioSequence,
 		default:
 			newIter, err = obiformats.WriteSequencesToStdout(iterator, opts...)
 		}
+
 	}
 
 	if err != nil {