Code reefactoring

pkg/obialign/pairedendalign.go

@@ -272,9 +272,9 @@ func PEAlign(seqA, seqB obiseq.BioSequence,
 	arena PEAlignArena) (int, []int) {
 	var score, shift int
 	var startA, startB int
-	var part_len, over int
+	var partLen, over int
-	var raw_seqA, qual_seqA []byte
+	var rawSeqA, qualSeqA []byte
-	var raw_seqB, qual_seqB []byte
+	var rawSeqB, qualSeqB []byte
 	var extra5, extra3 int
 
 	if !_InitializedDnaScore {
@@ -286,7 +286,7 @@ func PEAlign(seqA, seqB obiseq.BioSequence,
 		&arena.pointer.fastIndex,
 		&arena.pointer.fastBuffer)
 
-	shift, fast_score := obikmer.FastShiftFourMer(index, seqB, nil)
+	shift, fastScore := obikmer.FastShiftFourMer(index, seqB, nil)
 
 	if shift > 0 {
 		over = seqA.Length() - shift
@@ -294,7 +294,7 @@ func PEAlign(seqA, seqB obiseq.BioSequence,
 		over = seqB.Length() + shift
 	}
 
-	if fast_score+3 < over {
+	if fastScore+3 < over {
 		if shift > 0 {
 			startA = shift - delta
 			if startA < 0 {
@@ -302,14 +302,14 @@ func PEAlign(seqA, seqB obiseq.BioSequence,
 			}
 			extra5 = -startA
 			startB = 0
-			raw_seqA = seqA.Sequence()[startA:]
+			rawSeqA = seqA.Sequence()[startA:]
-			qual_seqA = seqA.Qualities()[startA:]
+			qualSeqA = seqA.Qualities()[startA:]
-			part_len = len(raw_seqA)
+			partLen = len(rawSeqA)
-			raw_seqB = seqB.Sequence()[0:part_len]
+			rawSeqB = seqB.Sequence()[0:partLen]
-			qual_seqB = seqB.Qualities()[0:part_len]
+			qualSeqB = seqB.Qualities()[0:partLen]
-			extra3 = seqB.Length() - part_len
+			extra3 = seqB.Length() - partLen
 			score = _FillMatrixPeLeftAlign(
-				raw_seqA, qual_seqA, raw_seqB, qual_seqB, gap,
+				rawSeqA, qualSeqA, rawSeqB, qualSeqB, gap,
 				&arena.pointer.scoreMatrix,
 				&arena.pointer.pathMatrix)
 		} else {
@@ -319,20 +319,20 @@ func PEAlign(seqA, seqB obiseq.BioSequence,
 				startB = 0
 			}
 			extra5 = startB
-			raw_seqB = seqB.Sequence()[startB:]
+			rawSeqB = seqB.Sequence()[startB:]
-			qual_seqB = seqB.Qualities()[startB:]
+			qualSeqB = seqB.Qualities()[startB:]
-			part_len = len(raw_seqB)
+			partLen = len(rawSeqB)
-			raw_seqA = seqA.Sequence()[:part_len]
+			rawSeqA = seqA.Sequence()[:partLen]
-			qual_seqA = seqA.Qualities()[:part_len]
+			qualSeqA = seqA.Qualities()[:partLen]
-			extra3 = part_len - seqA.Length()
+			extra3 = partLen - seqA.Length()
 			score = _FillMatrixPeRightAlign(
-				raw_seqA, qual_seqA, raw_seqB, qual_seqB, gap,
+				rawSeqA, qualSeqA, rawSeqB, qualSeqB, gap,
 				&arena.pointer.scoreMatrix,
 				&arena.pointer.pathMatrix)
 		}
 
 		arena.pointer.path = _Backtracking(arena.pointer.pathMatrix,
-			len(raw_seqA), len(raw_seqB),
+			len(rawSeqA), len(rawSeqB),
 			&arena.pointer.path)
 
 	} else {
@@ -340,27 +340,27 @@ func PEAlign(seqA, seqB obiseq.BioSequence,
 			startA = shift
 			startB = 0
 			extra5 = -startA
-			qual_seqA = seqA.Qualities()[startA:]
+			qualSeqA = seqA.Qualities()[startA:]
-			part_len = len(qual_seqA)
+			partLen = len(qualSeqA)
-			qual_seqB = seqB.Qualities()[0:part_len]
+			qualSeqB = seqB.Qualities()[0:partLen]
-			extra3 = seqB.Length() - part_len
+			extra3 = seqB.Length() - partLen
 			score = 0
 		} else {
 			startA = 0
 			startB = -shift
 			extra5 = startB
-			qual_seqB = seqB.Qualities()[startB:]
+			qualSeqB = seqB.Qualities()[startB:]
-			part_len = len(qual_seqB)
+			partLen = len(qualSeqB)
-			extra3 = part_len - seqA.Length()
+			extra3 = partLen - seqA.Length()
-			qual_seqA = seqA.Qualities()[:part_len]
+			qualSeqA = seqA.Qualities()[:partLen]
 		}
 		score = 0
-		for i, qualA := range qual_seqA {
+		for i, qualA := range qualSeqA {
-			qualB := qual_seqB[i]
+			qualB := qualSeqB[i]
 			score += _NucScorePartMatchMatch[qualA][qualB]
 		}
 		arena.pointer.path = arena.pointer.path[:0]
-		arena.pointer.path = append(arena.pointer.path, 0, part_len)
+		arena.pointer.path = append(arena.pointer.path, 0, partLen)
 	}
 
 	arena.pointer.path[0] += extra5

pkg/obiapat/pcr.go

@@ -195,7 +195,7 @@ func __pcr__(seq ApatSequence, sequence obiseq.BioSequence,
 
 								match, _ := sequence.Subsequence(fm[0], fm[1], opt.pointer.circular)
 								annot["forward_match"] = match.String()
-								match.Revoke()
+								match.Destroy()
 
 								annot["forward_error"] = erri
 
@@ -203,7 +203,7 @@ func __pcr__(seq ApatSequence, sequence obiseq.BioSequence,
 								match, _ = sequence.Subsequence(rm[0], rm[1], opt.pointer.circular)
 								match = match.ReverseComplement(true)
 								annot["reverse_match"] = match.String()
-								match.Revoke()
+								match.Destroy()
 
 								annot["reverse_error"] = errj
 								results = append(results, amplicon)
@@ -269,14 +269,14 @@ func __pcr__(seq ApatSequence, sequence obiseq.BioSequence,
 								match, _ := sequence.Subsequence(rm[0], rm[1], opt.pointer.circular)
 								match.ReverseComplement(true)
 								annot["forward_match"] = match.String()
-								match.Revoke()
+								match.Destroy()
 
 								annot["forward_error"] = errj
 
 								annot["reverse_primer"] = reverse.String()
 								match, _ = sequence.Subsequence(fm[0], fm[1], opt.pointer.circular)
 								annot["reverse_match"] = match.String()
-								match.Revoke()
+								match.Destroy()
 
 								annot["reverse_error"] = erri
 								results = append(results, amplicon)

pkg/obiformats/embl_read.go

@@ -16,15 +16,6 @@ import (
 
 var __FILE_CHUNK_SIZE__ = 1 << 20
 
-func __slice_grow__(slice []string) []string {
-	return slice
-}
-
-type __embl_chunk__ struct {
-	entries [][]string
-	order   int
-}
-
 type __file_chunk__ struct {
 	raw   io.Reader
 	order int

pkg/obiformats/fastseq_read.go

@@ -7,7 +7,6 @@ package obiformats
 import "C"
 
 import (
-	"errors"
 	"fmt"
 	"log"
 	"os"
@@ -89,7 +88,7 @@ func ReadFastSeqBatchFromFile(filename string, options ...WithOption) (obiseq.IB
 	err = nil
 
 	if pointer == nil {
-		err = errors.New(fmt.Sprintf("Cannot open file %s", filename))
+		err = fmt.Errorf("cannot open file %s", filename)
 		return obiseq.NilIBioSequenceBatch, err
 	}
 

pkg/obiformats/ncbitaxdump/read.go

@@ -3,7 +3,6 @@ package ncbitaxdump
 import (
 	"bufio"
 	"encoding/csv"
-	"errors"
 	"fmt"
 	"io"
 	"log"
@@ -95,8 +94,8 @@ func LoadNCBITaxDump(directory string, onlysn bool) (*obitax.Taxonomy, error) {
 
 	nodefile, err := os.Open(path.Join(directory, "nodes.dmp"))
 	if err != nil {
-		return nil, errors.New(fmt.Sprintf("Cannot open nodes file from '%s'",
+		return nil, fmt.Errorf("cannot open nodes file from '%s'",
-			directory))
+			directory)
 	}
 	defer nodefile.Close()
 
@@ -112,8 +111,8 @@ func LoadNCBITaxDump(directory string, onlysn bool) (*obitax.Taxonomy, error) {
 
 	namefile, nerr := os.Open(path.Join(directory, "names.dmp"))
 	if nerr != nil {
-		return nil, errors.New(fmt.Sprintf("Cannot open names file from '%s'",
+		return nil, fmt.Errorf("cannot open names file from '%s'",
-			directory))
+			directory)
 	}
 	defer namefile.Close()
 
@@ -128,8 +127,8 @@ func LoadNCBITaxDump(directory string, onlysn bool) (*obitax.Taxonomy, error) {
 
 	aliasfile, aerr := os.Open(path.Join(directory, "merged.dmp"))
 	if aerr != nil {
-		return nil, errors.New(fmt.Sprintf("Cannot open merged file from '%s'",
+		return nil, fmt.Errorf("cannot open merged file from '%s'",
-			directory))
+			directory)
 	}
 	defer aliasfile.Close()
 

pkg/obioptions/options.go

@@ -8,7 +8,6 @@ import (
 )
 
 var __debug__ = false
-var __profiling__ = ""
 
 type ArgumentParser func([]string) (*getoptions.GetOpt, []string, error)
 
@@ -16,7 +15,6 @@ func GenerateOptionParser(optionset ...func(*getoptions.GetOpt)) ArgumentParser
 	options := getoptions.New()
 	options.Bool("help", false, options.Alias("h", "?"))
 	options.BoolVar(&__debug__, "debug", false)
-	// options.StringVar(&__profiling__, "profile", "")
 
 	for _, o := range optionset {
 		o(options)
@@ -27,7 +25,7 @@ func GenerateOptionParser(optionset ...func(*getoptions.GetOpt)) ArgumentParser
 		remaining, err := options.Parse(args[1:])
 
 		if options.Called("help") {
-			fmt.Fprintf(os.Stderr, options.Help())
+			fmt.Fprint(os.Stderr, options.Help())
 			os.Exit(1)
 		}
 		return options, remaining, err

pkg/obiseq/join.go

@@ -1,19 +1,12 @@
 package obiseq
 
-import "git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
+func (sequence BioSequence) Join(seq2 BioSequence, inplace bool) BioSequence {
 
-func (sequence BioSequence) Join(seq2 BioSequence, copy_annot bool) (BioSequence, error) {
+	if !inplace {
-
+		sequence = sequence.Copy()
-	new_seq := MakeEmptyBioSequence()
-	new_seq.SetId(sequence.Id())
-	new_seq.SetDefinition(sequence.Definition())
-
-	new_seq.Write(sequence.Sequence())
-	new_seq.Write(seq2.Sequence())
-
-	if copy_annot {
-		goutils.CopyMap(new_seq.Annotations(), sequence.Annotations())
 	}
 
-	return new_seq, nil
+	sequence.Write(seq2.Sequence())
+
+	return sequence
 }

pkg/obitax/iterator.go

@@ -39,7 +39,7 @@ func (set *TaxonSlice) Iterator() *ITaxonSet {
 	return i
 }
 
-func (taxonmy *Taxonomy) iterator() *ITaxonSet {
+func (taxonmy *Taxonomy) Iterator() *ITaxonSet {
 	return taxonmy.nodes.Iterator()
 }
 

pkg/obitax/path.go

@@ -1,7 +1,6 @@
 package obitax
 
 import (
-	"errors"
 	"fmt"
 )
 
@@ -14,7 +13,7 @@ func (taxon *TaxNode) Path() (*TaxonSlice, error) {
 		taxon = taxon.pparent
 
 		if taxon == nil {
-			return nil, errors.New(fmt.Sprint("Taxonomy must be reindexed"))
+			return nil, fmt.Errorf("Taxonomy must be reindexed")
 		}
 
 		path = append(path, taxon)

pkg/obitax/taxonomy.go

@@ -1,7 +1,6 @@
 package obitax
 
 import (
-	"errors"
 	"fmt"
 	"log"
 )
@@ -42,15 +41,11 @@ func (taxonomy *Taxonomy) Length() int {
 	return len(*taxonomy.nodes)
 }
 
-func (taxonomy *Taxonomy) Iterator() *ITaxonSet {
-	return taxonomy.nodes.Iterator()
-}
-
 func (taxonomy *Taxonomy) AddNewTaxa(taxid, parent int, rank string, replace bool, init bool) (*TaxNode, error) {
 	if !replace {
 		_, ok := (*taxonomy.nodes)[taxid]
 		if ok {
-			return nil, errors.New(fmt.Sprintf("Trying to add taxoon %d already present in the taxonomy", taxid))
+			return nil, fmt.Errorf("trying to add taxoon %d already present in the taxonomy", taxid)
 		}
 	}
 
@@ -66,7 +61,7 @@ func (taxonomy *Taxonomy) Taxon(taxid int) (*TaxNode, error) {
 	if !ok {
 		a, aok := taxonomy.alias[taxid]
 		if !aok {
-			return nil, errors.New(fmt.Sprintf("Taxid %d is not part of the taxonomy", taxid))
+			return nil, fmt.Errorf("Taxid %d is not part of the taxonomy", taxid)
 		}
 		log.Printf("Taxid %d is deprecated and must be replaced by %d", taxid, a.taxid)
 		t = a
@@ -109,9 +104,9 @@ func (taxonomy *Taxonomy) ReindexParent() error {
 	for _, taxon := range *taxonomy.nodes {
 		taxon.pparent, ok = (*taxonomy.nodes)[taxon.parent]
 		if !ok {
-			return errors.New(fmt.Sprintf("Parent %d of taxon %d is not defined in taxonomy",
+			return fmt.Errorf("Parent %d of taxon %d is not defined in taxonomy",
 				taxon.taxid,
-				taxon.parent))
+				taxon.parent)
 		}
 	}
 

pkg/obitools/obiconvert/sequence_reader.go

@@ -17,24 +17,24 @@ func __expand_list_of_files__(check_ext bool, filenames ...string) ([]string, er
 
 		err = filepath.Walk(fn,
 			func(path string, info os.FileInfo, err error) error {
-
+				var e error
 				for info.Mode()&os.ModeSymlink == os.ModeSymlink {
-					path, err = filepath.EvalSymlinks(path)
+					path, e = filepath.EvalSymlinks(path)
-					if err != nil {
+					if e != nil {
-						return err
+						return e
 					}
 
-					info, err = os.Stat(path)
+					info, e = os.Stat(path)
-					if err != nil {
+					if e != nil {
-						return err
+						return e
 					}
 				}
 
 				if info.IsDir() {
 					if path != fn {
-						subdir, err := __expand_list_of_files__(true, path)
+						subdir, e := __expand_list_of_files__(true, path)
-						if err != nil {
+						if e != nil {
-							return err
+							return e
 						}
 						list_of_files = append(list_of_files, subdir...)
 					} else {

pkg/obitools/obifind/options.go

@@ -86,7 +86,7 @@ func LoadSelectedTaxonomy() (*obitax.Taxonomy, error) {
 		return __selected_taxonomy__, nil
 	}
 
-	return nil, errors.New("No NCBII taxdump selected using option -t|--taxdump")
+	return nil, errors.New("no NCBI taxdump selected using option -t|--taxdump")
 }
 
 func OptionSet(options *getoptions.GetOpt) {

pkg/obitools/obipairing/pairing.go

@@ -153,6 +153,8 @@ func IAssemblePESequencesBatch(iterator obiseq.IPairedBioSequenceBatch,
 					bar.Add(59)
 					processed += 59
 				}
+				A.Destroy()
+				B.Destroy()
 			}
 			bar.Add(batch.Length() - processed)
 			new_iter.Channel() <- obiseq.MakeBioSequenceBatch(