move the worker class to the obiseq package

cmd/obitools/obicomplement/main.go

@@ -3,7 +3,7 @@ package main
 import (
 	"os"
 
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
@@ -16,6 +16,6 @@ func main() {
 
 	fs, _ := obiconvert.ReadBioSequences(args...)
 
-	comp := fs.MakeIWorker(obiiter.ReverseComplementWorker(true))
+	comp := fs.MakeIWorker(obiseq.ReverseComplementWorker(true))
 	obiconvert.WriteBioSequences(comp, true)
 }

pkg/obiapat/pcr.go

@@ -4,7 +4,6 @@ import (
 	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 )
 
@@ -441,7 +440,7 @@ func PCRSlice(sequences obiseq.BioSequenceSlice,
 
 // PCRSliceWorker is a worker function builder which produce
 // job function usable by the obiseq.MakeISliceWorker function.
-func PCRSliceWorker(options ...WithOption) obiiter.SeqSliceWorker {
+func PCRSliceWorker(options ...WithOption) obiseq.SeqSliceWorker {
 
 	opt := MakeOptions(options)
 	worker := func(sequences obiseq.BioSequenceSlice) obiseq.BioSequenceSlice {

pkg/obiformats/fastseq_header.go

@@ -18,7 +18,7 @@ func ParseGuessedFastSeqHeader(sequence *obiseq.BioSequence) {
 func IParseFastSeqHeaderBatch(iterator obiiter.IBioSequence,
 	options ...WithOption) obiiter.IBioSequence {
 	opt := MakeOptions(options)
-	return iterator.MakeIWorker(obiiter.AnnotatorToSeqWorker(opt.ParseFastSeqHeader()),
+	return iterator.MakeIWorker(obiseq.AnnotatorToSeqWorker(opt.ParseFastSeqHeader()),
 		opt.ParallelWorkers(),
 		opt.BufferSize())
 }

pkg/obiformats/options.go

@@ -1,12 +1,11 @@
 package obiformats
 
 import (
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 )
 
 type __options__ struct {
-	fastseq_header_parser obiiter.SeqAnnotator
+	fastseq_header_parser obiseq.SeqAnnotator
 	fastseq_header_writer func(*obiseq.BioSequence) string
 	with_progress_bar     bool
 	buffer_size           int
@@ -59,7 +58,7 @@ func (opt Options) ParallelWorkers() int {
 	return opt.pointer.parallel_workers
 }
 
-func (opt Options) ParseFastSeqHeader() obiiter.SeqAnnotator {
+func (opt Options) ParseFastSeqHeader() obiseq.SeqAnnotator {
 	return opt.pointer.fastseq_header_parser
 }
 
@@ -124,7 +123,7 @@ func OptionsQualitySolexa() WithOption {
 	return OptionsQualityShift(64)
 }
 
-func OptionsFastSeqHeaderParser(parser obiiter.SeqAnnotator) WithOption {
+func OptionsFastSeqHeaderParser(parser obiseq.SeqAnnotator) WithOption {
 	f := WithOption(func(opt Options) {
 		opt.pointer.fastseq_header_parser = parser
 	})

pkg/obiiter/batchiterator.go

@@ -1,3 +1,5 @@
+// It takes a slice of BioSequence objects, and returns an iterator that will return batches of
+// BioSequence objects
 package obiiter
 
 import (

pkg/obiiter/workers.go

@@ -6,18 +6,6 @@ import (
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 )
 
-type SeqAnnotator func(*obiseq.BioSequence)
-
-type SeqWorker func(*obiseq.BioSequence) *obiseq.BioSequence
-type SeqSliceWorker func(obiseq.BioSequenceSlice) obiseq.BioSequenceSlice
-
-func AnnotatorToSeqWorker(function SeqAnnotator) SeqWorker {
-	f := func(seq *obiseq.BioSequence) *obiseq.BioSequence {
-		function(seq)
-		return seq
-	}
-	return f
-}
 
 // That method allows for applying a SeqWorker function on every sequences.
 //
@@ -27,7 +15,7 @@ func AnnotatorToSeqWorker(function SeqAnnotator) SeqWorker {
 // Moreover the SeqWorker function, the method accepted two optional integer parameters.
 //   - First is allowing to indicates the number of workers running in parallele (default 4)
 //   - The second the size of the chanel buffer. By default set to the same value than the input buffer.
-func (iterator IBioSequence) MakeIWorker(worker SeqWorker, sizes ...int) IBioSequence {
+func (iterator IBioSequence) MakeIWorker(worker obiseq.SeqWorker, sizes ...int) IBioSequence {
 	nworkers := 4
 	buffsize := iterator.BufferSize()
 
@@ -70,7 +58,7 @@ func (iterator IBioSequence) MakeIWorker(worker SeqWorker, sizes ...int) IBioSeq
 }
 
 func (iterator IBioSequence) MakeIConditionalWorker(predicate obiseq.SequencePredicate,
-	worker SeqWorker, sizes ...int) IBioSequence {
+	worker obiseq.SeqWorker, sizes ...int) IBioSequence {
 	nworkers := 4
 	buffsize := iterator.BufferSize()
 
@@ -114,7 +102,7 @@ func (iterator IBioSequence) MakeIConditionalWorker(predicate obiseq.SequencePre
 	return newIter
 }
 
-func (iterator IBioSequence) MakeISliceWorker(worker SeqSliceWorker, sizes ...int) IBioSequence {
+func (iterator IBioSequence) MakeISliceWorker(worker obiseq.SeqSliceWorker, sizes ...int) IBioSequence {
 	nworkers := 4
 	buffsize := iterator.BufferSize()
 
@@ -153,7 +141,7 @@ func (iterator IBioSequence) MakeISliceWorker(worker SeqSliceWorker, sizes ...in
 	return newIter
 }
 
-func WorkerPipe(worker SeqWorker, sizes ...int) Pipeable {
+func WorkerPipe(worker obiseq.SeqWorker, sizes ...int) Pipeable {
 	f := func(iterator IBioSequence) IBioSequence {
 		return iterator.MakeIWorker(worker, sizes...)
 	}
@@ -161,7 +149,7 @@ func WorkerPipe(worker SeqWorker, sizes ...int) Pipeable {
 	return f
 }
 
-func SliceWorkerPipe(worker SeqSliceWorker, sizes ...int) Pipeable {
+func SliceWorkerPipe(worker obiseq.SeqSliceWorker, sizes ...int) Pipeable {
 	f := func(iterator IBioSequence) IBioSequence {
 		return iterator.MakeISliceWorker(worker, sizes...)
 	}
@@ -169,10 +157,3 @@ func SliceWorkerPipe(worker SeqSliceWorker, sizes ...int) Pipeable {
 	return f
 }
 
-func ReverseComplementWorker(inplace bool) SeqWorker {
-	f := func(input *obiseq.BioSequence) *obiseq.BioSequence {
-		return input.ReverseComplement(inplace)
-	}
-
-	return f
-}

pkg/obingslibrary/worker.go

@@ -1,7 +1,6 @@
 package obingslibrary
 
 import (
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 )
 
@@ -170,7 +169,7 @@ func ExtractBarcodeSlice(ngslibrary NGSLibrary,
 }
 
 func ExtractBarcodeSliceWorker(ngslibrary NGSLibrary,
-	options ...WithOption) obiiter.SeqSliceWorker {
+	options ...WithOption) obiseq.SeqSliceWorker {
 
 	opt := MakeOptions(options)
 

pkg/obiseq/revcomp.go

@@ -64,3 +64,12 @@ func (sequence *BioSequence) _revcmpMutation() *BioSequence {
 
 	return sequence
 }
+
+
+func ReverseComplementWorker(inplace bool) SeqWorker {
+	f := func(input *BioSequence) *BioSequence {
+		return input.ReverseComplement(inplace)
+	}
+
+	return f
+}

pkg/obiseq/worker.go

@@ -0,0 +1,31 @@
+package obiseq
+
+type SeqAnnotator func(*BioSequence)
+
+type SeqWorker func(*BioSequence) *BioSequence
+type SeqSliceWorker func(BioSequenceSlice) BioSequenceSlice
+
+func AnnotatorToSeqWorker(function SeqAnnotator) SeqWorker {
+	f := func(seq *BioSequence) *BioSequence {
+		function(seq)
+		return seq
+	}
+	return f
+}
+
+func SeqToSliceWorker(worker SeqWorker, inplace bool) SeqSliceWorker {
+	f := func(input BioSequenceSlice) BioSequenceSlice {
+		output := input
+		if (! inplace) {
+			output = MakeBioSequenceSlice() 
+		}
+			for i,s := range(input) {
+				output[i] = worker(s)
+			}
+
+		return output
+	}
+
+	return f
+}
+

pkg/obitax/sequence_workers.go

@@ -2,12 +2,11 @@ package obitax
 
 import (
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
-	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 	log "github.com/sirupsen/logrus"
 )
 
-func (taxonomy *Taxonomy) MakeSetTaxonAtRankWorker(rank string) obiiter.SeqWorker {
+func (taxonomy *Taxonomy) MakeSetTaxonAtRankWorker(rank string) obiseq.SeqWorker {
 
 	if !goutils.Contains(taxonomy.RankList(), rank) {
 		log.Fatalf("%s is not a valid rank (allowed ranks are %v)",
@@ -23,7 +22,7 @@ func (taxonomy *Taxonomy) MakeSetTaxonAtRankWorker(rank string) obiiter.SeqWorke
 	return w
 }
 
-func (taxonomy *Taxonomy) MakeSetSpeciesWorker() obiiter.SeqWorker {
+func (taxonomy *Taxonomy) MakeSetSpeciesWorker() obiseq.SeqWorker {
 
 	w := func(sequence *obiseq.BioSequence) *obiseq.BioSequence {
 		taxonomy.SetSpecies(sequence)
@@ -33,7 +32,7 @@ func (taxonomy *Taxonomy) MakeSetSpeciesWorker() obiiter.SeqWorker {
 	return w
 }
 
-func (taxonomy *Taxonomy) MakeSetGenusWorker() obiiter.SeqWorker {
+func (taxonomy *Taxonomy) MakeSetGenusWorker() obiseq.SeqWorker {
 
 	w := func(sequence *obiseq.BioSequence) *obiseq.BioSequence {
 		taxonomy.SetGenus(sequence)
@@ -43,7 +42,7 @@ func (taxonomy *Taxonomy) MakeSetGenusWorker() obiiter.SeqWorker {
 	return w
 }
 
-func (taxonomy *Taxonomy) MakeSetFamilyWorker() obiiter.SeqWorker {
+func (taxonomy *Taxonomy) MakeSetFamilyWorker() obiseq.SeqWorker {
 
 	w := func(sequence *obiseq.BioSequence) *obiseq.BioSequence {
 		taxonomy.SetFamily(sequence)
@@ -52,5 +51,3 @@ func (taxonomy *Taxonomy) MakeSetFamilyWorker() obiiter.SeqWorker {
 
 	return w
 }
-
-

pkg/obitools/obiannotate/options.go

@@ -0,0 +1,93 @@
+package obiannotate
+
+import (
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obigrep"
+	"github.com/DavidGamba/go-getoptions"
+)
+
+var _addRank = false
+var _toBeRenamed = make(map[string]string, 0)
+var _toBeDeleted = make([]string, 0)
+var _keepOnly = make([]string, 0)
+var _taxonAtRank = make([]string, 0)
+var _tagList = ""
+var _clearAll = false
+var _setSeqLength = false
+var _uniqueID = false
+
+func SequenceSelectionOptionSet(options *getoptions.GetOpt) {
+	options.BoolVar(&_addRank, "seq-rank", _addRank,
+		options.Description("Adds a new attribute named seq_rank to the sequence record indicating its entry number in the sequence file."),
+	)
+
+	options.BoolVar(&_clearAll, "clear", _clearAll,
+		options.Alias("C"),
+		options.Description("Clears all attributes associated to the sequence records."),
+	)
+
+	options.BoolVar(&_setSeqLength, "length", _setSeqLength,
+		options.Description("Adds attribute with seq_length as a key and sequence length as a value."),
+	)
+
+	options.BoolVar(&_uniqueID, "uniq-id", _uniqueID,
+		options.Description("Forces sequence record ids to be unique."),
+	)
+	options.StringMapVar(&_toBeRenamed, "rename-tag", 1, 1,
+		options.Alias("R"),
+		options.ArgName("NEW_NAME=OLD_NAME"),
+		options.Description("Changes attribute name <OLD_NAME> to <NEW_NAME>. When attribute named <OLD_NAME>"+
+			" is missing, the sequence record is skipped and the next one is examined."))
+
+	options.StringSliceVar(&_toBeDeleted, "delete-tag", 1, 1,
+		options.ArgName("KEY"),
+		options.Description(" Deletes attribute named <KEY>.When this attribute is missing,"+
+			" the sequence record is skipped and the next one is examined."))
+
+	options.StringSliceVar(&_taxonAtRank, "with-taxon-at-rank", 1, 1,
+		options.ArgName("RANK_NAME"),
+		options.Description("Adds taxonomic annotation at taxonomic rank <RANK_NAME>."))
+
+	options.StringVar(&_tagList, "tag-list", _tagList,
+		options.ArgName("FILENAME"),
+		options.Description("<FILENAME> points to a file containing attribute names"+
+			" and values to modify for specified sequence records."))
+
+	options.StringSliceVar(&_keepOnly, "keep", 1, 1,
+		options.Alias("k"),
+		options.ArgName("KEY"),
+		options.Description("Keeps only attribute with key <KEY>. Several -k options can be combined."))
+
+}
+
+// OptionSet adds to the basic option set every options declared for
+// the obipcr command
+func OptionSet(options *getoptions.GetOpt) {
+	obiconvert.OptionSet(options)
+	obigrep.SequenceSelectionOptionSet(options)
+	SequenceSelectionOptionSet(options)
+}
+
+// -S <KEY>:<PYTHON_EXPRESSION>, --set-tag=<KEY>:<PYTHON_EXPRESSION>
+// Creates a new attribute named with a key <KEY> and a value computed from <PYTHON_EXPRESSION>.
+
+// --set-identifier=<PYTHON_EXPRESSION>
+// Sets sequence record identifier with a value computed from <PYTHON_EXPRESSION>.
+
+// --run=<PYTHON_EXPRESSION>
+// Runs a python expression on each selected sequence.
+
+// --set-sequence=<PYTHON_EXPRESSION>
+// Changes the sequence itself with a value computed from <PYTHON_EXPRESSION>.
+
+// -T, --set-definition=<PYTHON_EXPRESSION>
+// Sets sequence definition with a value computed from <PYTHON_EXPRESSION>.
+
+// -O, --only-valid-python
+// Allows only valid python expressions.
+
+// -m <MCLFILE>, --mcl=<MCLFILE>
+// Creates a new attribute containing the number of the cluster the sequence record was assigned to, as indicated in file <MCLFILE>.
+
+// --uniq-id
+// Forces sequence record ids to be unique.

pkg/obitools/obitag/obitag.go

@@ -165,7 +165,7 @@ func Identify(sequence *obiseq.BioSequence,
 func IdentifySeqWorker(references obiseq.BioSequenceSlice,
 	refcounts []*obikmer.Table4mer,
 	taxo *obitax.Taxonomy,
-	runExact bool) obiiter.SeqWorker {
+	runExact bool) obiseq.SeqWorker {
 	return func(sequence *obiseq.BioSequence) *obiseq.BioSequence {
 		return Identify(sequence, references, refcounts, taxo, runExact)
 	}