obitools/obitools4
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Change path of the obitools pkg

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Former-commit-id: 311cbf8df3b990b393c6f4885d62e74564423b65
This commit is contained in:
Eric Coissac
2023-11-29 12:14:37 +01:00
parent 72ad84c2d4
commit 8d77cc4133
122 changed files with 1004 additions and 544 deletions
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2
pkg/obialign/alignment.go
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@ -9,7 +9,7 @@ import (
"math"
"strings"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
)
// // A pool of byte slices.

4
pkg/obialign/fastlcs.go
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@ -1,8 +1,8 @@
package obialign
// import (
// "git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
// "git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
// "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
// "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
// )
const wsize = 16

4
pkg/obialign/fastlcsegf.go
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@ -1,8 +1,8 @@
package obialign
import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
)
var _iupac = [26]byte{

2
pkg/obialign/fourbitsencode.go
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@ -1,7 +1,7 @@
package obialign
import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
)
var _FourBitsBaseCode = []byte{0b0000,

2
pkg/obialign/is_d0_or_d1.go
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@ -1,6 +1,6 @@
package obialign
import "git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
import "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
func abs(x int) int {
if x < 0 {

4
pkg/obialign/pairedendalign.go
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@ -3,8 +3,8 @@ package obialign
import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obikmer"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obikmer"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
)
type _PeAlignArena struct {

6
pkg/obiapat/pattern.go
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@ -13,9 +13,9 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obialign"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obialign"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
)
var _MaxPatLen = int(C.MAX_PAT_LEN)

4
pkg/obiapat/pcr.go
View File

@ -3,8 +3,8 @@ package obiapat
import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
)
type _Options struct {

7
pkg/obichunk/chunk_on_disk.go
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@ -8,9 +8,9 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
)
func tempDir() (string, error) {
@ -42,7 +42,6 @@ func ISequenceChunkOnDisk(iterator obiiter.IBioSequence,
return obiiter.NilIBioSequence, err
}
newIter := obiiter.MakeIBioSequence()
newIter.Add(1)

4
pkg/obichunk/chunks.go
View File

@ -5,8 +5,8 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
)
func ISequenceChunk(iterator obiiter.IBioSequence,

6
pkg/obichunk/subchunks.go
View File

@ -6,9 +6,9 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
)
//

4
pkg/obichunk/unique.go
View File

@ -5,8 +5,8 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
)
// Runs dereplication algorithm on a obiiter.IBioSequenceBatch

6
pkg/obicorazick/worker.go
View File

@ -3,14 +3,14 @@ package obicorazick
import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"github.com/rrethy/ahocorasick"
)
func AhoCorazickWorker(slot string, patterns []string) obiseq.SeqWorker {
matcher := ahocorasick.CompileStrings(patterns)
fslot := slot + "_Fwd"
rslot := slot + "_Rev"
@ -18,7 +18,7 @@ func AhoCorazickWorker(slot string, patterns []string) obiseq.SeqWorker {
matchesF := len(matcher.FindAllByteSlice(s.Sequence()))
matchesR := len(matcher.FindAllByteSlice(s.ReverseComplement(false).Sequence()))
log.Debugln("Macthes = ",matchesF,matchesR)
log.Debugln("Macthes = ", matchesF, matchesR)
matches := matchesF + matchesR
if matches > 0 {
s.SetAttribute(slot, matches)

6
pkg/obiformats/batch_of_files_reader.go
View File

@ -3,8 +3,8 @@ package obiformats
import (
"log"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
)
func ReadSequencesBatchFromFiles(filenames []string,
@ -48,8 +48,6 @@ func ReadSequencesBatchFromFiles(filenames []string,
log.Printf("Start reading of file : %s", filename)
for iter.Next() {
batch := iter.Get()
batchiter.Push(batch.Reorder(nextCounter()))

2
pkg/obiformats/batch_reader_type.go
View File

@ -1,5 +1,5 @@
package obiformats
import "git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
import "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
type IBatchReader func(string, ...WithOption) (obiiter.IBioSequence, error)

8
pkg/obiformats/csv_writer.go
View File

@ -9,10 +9,10 @@ import (
"sync"
"time"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
log "github.com/sirupsen/logrus"
)

2
pkg/obiformats/dispatcher.go
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@ -10,7 +10,7 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
)
type SequenceBatchWriterToFile func(iterator obiiter.IBioSequence,

6
pkg/obiformats/ecopcr_read.go
View File

@ -13,9 +13,9 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
)
type __ecopcr_file__ struct {

6
pkg/obiformats/embl_read.go
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@ -10,9 +10,9 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
)
var _FileChunkSize = 1 << 28

2
pkg/obiformats/empty_file.go
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@ -1,6 +1,6 @@
package obiformats
import "git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
import "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
func ReadEmptyFile(options ...WithOption) (obiiter.IBioSequence, error) {
out := obiiter.MakeIBioSequence()

8
pkg/obiformats/fastaseq_read.go
View File

@ -7,10 +7,10 @@ import (
"os"
"path"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
"golang.org/x/exp/slices"
log "github.com/sirupsen/logrus"

8
pkg/obiformats/fastqseq_read.go
View File

@ -6,10 +6,10 @@ import (
"os"
"path"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
log "github.com/sirupsen/logrus"
"golang.org/x/exp/slices"
)

4
pkg/obiformats/fastseq_header.go
View File

@ -3,8 +3,8 @@ package obiformats
import (
"strings"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
)
// ParseGuessedFastSeqHeader parses the guessed fast sequence header.

2
pkg/obiformats/fastseq_interface.go
View File

@ -1,5 +1,5 @@
package obiformats
import "git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
import "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
type FormatHeader func(sequence *obiseq.BioSequence) string

4
pkg/obiformats/fastseq_json_header.go
View File

@ -6,8 +6,8 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
"github.com/goccy/go-json"
)

4
pkg/obiformats/fastseq_obi_header.go
View File

@ -9,8 +9,8 @@ import (
"strconv"
"strings"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
"github.com/goccy/go-json"
)

8
pkg/obiformats/fastseq_read.go
View File

@ -14,10 +14,10 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
)
func _FastseqReader(source string,

6
pkg/obiformats/fastseq_write_fasta.go
View File

@ -12,9 +12,9 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
)
// min returns the minimum of two integers.

8
pkg/obiformats/fastseq_write_fastq.go
View File

@ -10,10 +10,10 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
)
// The function FormatFastq takes a BioSequence object, a quality shift value, and a header formatter

6
pkg/obiformats/genbank_read.go
View File

@ -11,9 +11,9 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
)
type gbstate int

6
pkg/obiformats/json_writer.go
View File

@ -11,9 +11,9 @@ import (
"sync"
"time"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
log "github.com/sirupsen/logrus"
)

2
pkg/obiformats/ncbitaxdump/read.go
View File

@ -12,7 +12,7 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitax"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
)
func loadNodeTable(reader io.Reader, taxonomy *obitax.Taxonomy) {

4
pkg/obiformats/ngsfilter_read.go
View File

@ -6,8 +6,8 @@ import (
"io"
"strings"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obingslibrary"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obingslibrary"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
)
func _readLines(reader io.Reader) []string {

4
pkg/obiformats/options.go
View File

@ -1,8 +1,8 @@
package obiformats
import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
)
type __options__ struct {

4
pkg/obiformats/universal_read.go
View File

@ -11,8 +11,8 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
)
// OBIMimeTypeGuesser is a function that takes an io.Reader as input and guesses the MIME type of the data.

2
pkg/obiformats/universal_write.go
View File

@ -7,7 +7,7 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
)
func WriteSequence(iterator obiiter.IBioSequence,

2
pkg/obiiter/batch.go
View File

@ -1,6 +1,6 @@
package obiiter
import "git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
import "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
type BioSequenceBatch struct {
slice obiseq.BioSequenceSlice

6
pkg/obiiter/batchiterator.go
View File

@ -10,9 +10,9 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
"github.com/tevino/abool/v2"
)

4
pkg/obiiter/distribute.go
View File

@ -4,7 +4,7 @@ import (
"fmt"
"sync"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
)
type IDistribute struct {
@ -46,8 +46,6 @@ func (iterator IBioSequence) Distribute(class *obiseq.BioSequenceClassifier, siz
batchsize = sizes[0]
}
jobDone := sync.WaitGroup{}
lock := sync.Mutex{}

10
pkg/obiiter/fragment.go
View File

@ -3,8 +3,8 @@ package obiiter
import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
)
func IFragments(minsize, length, overlap, size, nworkers int) Pipeable {
@ -25,19 +25,19 @@ func IFragments(minsize, length, overlap, size, nworkers int) Pipeable {
news := obiseq.MakeBioSequenceSlice()
sl := iterator.Get()
for _, s := range sl.Slice() {
if s.Len() <= minsize {
news = append(news, s)
} else {
for i := 0; i < s.Len(); i += step {
end := obiutils.MinInt(i+length, s.Len())
fusion:=false
fusion := false
if (s.Len() - end) < step {
end = s.Len()
fusion = true
}
frg, err := s.Subsequence(i, end, false)
if err != nil {
log.Panicln(err)
}

2
pkg/obiiter/merge.go
View File

@ -1,6 +1,6 @@
package obiiter
import "git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
import "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
func (iterator IBioSequence) IMergeSequenceBatch(na string, statsOn []string, sizes ...int) IBioSequence {
batchsize := 100

48
pkg/obiiter/workers.go
View File

@ -3,8 +3,8 @@ package obiiter
import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
)
// That method allows for applying a SeqWorker function on every sequences.
@ -56,6 +56,16 @@ func (iterator IBioSequence) MakeIWorker(worker obiseq.SeqWorker, sizes ...int)
return newIter
}
// MakeIConditionalWorker applies a given worker function to each sequence in the iterator that satisfies the given predicate.
// It creates a new iterator with the modified sequences and returns it.
//
// Parameters:
// - predicate: A function that takes a sequence and returns a boolean value indicating whether the sequence satisfies a certain condition.
// - worker: A function that takes a sequence and returns a modified version of the sequence.
// - sizes: Optional. One or more integers representing the number of workers to be used for parallel processing. If not provided, the number of workers will be determined by the obioptions.CLIReadParallelWorkers() function.
//
// Return:
// - newIter: A new IBioSequence iterator with the modified sequences.
func (iterator IBioSequence) MakeIConditionalWorker(predicate obiseq.SequencePredicate,
worker obiseq.SeqWorker, sizes ...int) IBioSequence {
nworkers := obioptions.CLIReadParallelWorkers()
@ -100,6 +110,16 @@ func (iterator IBioSequence) MakeIConditionalWorker(predicate obiseq.SequencePre
return newIter
}
// MakeISliceWorker applies a SeqSliceWorker function to each slice in the IBioSequence iterator,
// creating a new IBioSequence with the modified slices.
//
// The worker function takes a slice as input and returns a modified slice. It is applied to each
// slice in the iterator.
//
// The sizes argument is optional and specifies the number of workers to use. If sizes is not
// provided, the default number of workers is used.
//
// The function returns a new IBioSequence containing the modified slices.
func (iterator IBioSequence) MakeISliceWorker(worker obiseq.SeqSliceWorker, sizes ...int) IBioSequence {
nworkers := obioptions.CLIParallelWorkers()
@ -119,12 +139,12 @@ func (iterator IBioSequence) MakeISliceWorker(worker obiseq.SeqSliceWorker, size
f := func(iterator IBioSequence) {
for iterator.Next() {
batch := iterator.Get()
bs := len(batch.slice)
batch.slice = worker(batch.slice)
if bs != len(batch.slice) {
log.Warnf("Input size : %d output %d", bs, len(batch.slice))
if batch.slice.Len() > 0 {
newIter.Push(batch)
} else {
batch.Recycle(false)
}
newIter.Push(batch)
}
newIter.Done()
}
@ -142,6 +162,17 @@ func (iterator IBioSequence) MakeISliceWorker(worker obiseq.SeqSliceWorker, size
return newIter
}
// WorkerPipe is a function that takes a SeqWorker and a variadic list of sizes as parameters and returns a Pipeable.
//
// The WorkerPipe function creates a closure that takes an IBioSequence iterator as a parameter and returns an IBioSequence.
// Inside the closure, the MakeIWorker method of the iterator is called with the provided worker and sizes, and the result is returned.
//
// Parameters:
// - worker: A SeqWorker object that represents the worker to be used in the closure.
// - sizes: A variadic list of int values that represents the sizes to be used in the MakeIWorker method.
//
// Return:
// - f: A Pipeable object that represents the closure created by the WorkerPipe function.
func WorkerPipe(worker obiseq.SeqWorker, sizes ...int) Pipeable {
f := func(iterator IBioSequence) IBioSequence {
return iterator.MakeIWorker(worker, sizes...)
@ -150,6 +181,11 @@ func WorkerPipe(worker obiseq.SeqWorker, sizes ...int) Pipeable {
return f
}
// SliceWorkerPipe creates a Pipeable function that applies a SeqSliceWorker to an iterator.
//
// The worker parameter is the SeqSliceWorker to be applied.
// The sizes parameter is a variadic parameter representing the sizes of the slices.
// The function returns a Pipeable function that applies the SeqSliceWorker to the iterator.
func SliceWorkerPipe(worker obiseq.SeqSliceWorker, sizes ...int) Pipeable {
f := func(iterator IBioSequence) IBioSequence {
return iterator.MakeISliceWorker(worker, sizes...)

4
pkg/obikmer/counting.go
View File

@ -3,8 +3,8 @@ package obikmer
import (
"math"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
)
type Table4mer [256]uint16

2
pkg/obikmer/debruijn.go
View File

@ -6,7 +6,7 @@ import (
"math"
"math/bits"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"github.com/daichi-m/go18ds/sets/linkedhashset"
"github.com/daichi-m/go18ds/stacks/arraystack"
)

2
pkg/obikmer/encodefourmer.go
View File

@ -1,7 +1,7 @@
package obikmer
import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
)
var __single_base_code__ = []byte{0,

6
pkg/obingslibrary/match.go
View File

@ -7,9 +7,9 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiapat"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiapat"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
)
type DemultiplexMatch struct {

4
pkg/obingslibrary/ngslibrary.go
View File

@ -1,8 +1,8 @@
package obingslibrary
import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiapat"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiapat"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
)
type PrimerPair struct {

6
pkg/obingslibrary/worker.go
View File

@ -1,7 +1,7 @@
package obingslibrary
import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
)
type _Options struct {
@ -159,7 +159,7 @@ func ExtractBarcodeSlice(ngslibrary NGSLibrary,
opt := MakeOptions(options)
ngslibrary.Compile(opt.AllowedMismatch(),opt.AllowsIndel())
ngslibrary.Compile(opt.AllowedMismatch(), opt.AllowsIndel())
return _ExtractBarcodeSlice(ngslibrary, sequences, opt)
}
@ -169,7 +169,7 @@ func ExtractBarcodeSliceWorker(ngslibrary NGSLibrary,
opt := MakeOptions(options)
ngslibrary.Compile(opt.AllowedMismatch(),opt.AllowsIndel())
ngslibrary.Compile(opt.AllowedMismatch(), opt.AllowsIndel())
worker := func(sequences obiseq.BioSequenceSlice) obiseq.BioSequenceSlice {
return _ExtractBarcodeSlice(ngslibrary, sequences, opt)

2
pkg/obiseq/attributes.go
View File

@ -4,7 +4,7 @@ import (
"fmt"
"strconv"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
log "github.com/sirupsen/logrus"
)

4
pkg/obiseq/biosequence.go
View File

@ -15,8 +15,8 @@ import (
"sync"
"sync/atomic"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
log "github.com/sirupsen/logrus"
)

2
pkg/obiseq/biosequenceslice.go
View File

@ -3,7 +3,7 @@ package obiseq
import (
"sync"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
log "github.com/sirupsen/logrus"
"golang.org/x/exp/slices"
)

2
pkg/obiseq/class.go
View File

@ -6,7 +6,7 @@ import (
"strconv"
"sync"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
log "github.com/sirupsen/logrus"
)

2
pkg/obiseq/language.go
View File

@ -6,7 +6,7 @@ import (
"reflect"
"strings"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
"github.com/PaesslerAG/gval"
)

2
pkg/obiseq/merge.go
View File

@ -5,7 +5,7 @@ import (
"reflect"
"strings"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
log "github.com/sirupsen/logrus"
)

2
pkg/obiseq/pool.go
View File

@ -4,7 +4,7 @@ import (
"log"
"sync"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
)
var _BioSequenceByteSlicePool = sync.Pool{

4
pkg/obisuffix/suffix_array.go
View File

@ -5,8 +5,8 @@ import (
"fmt"
"sort"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
)
type Suffix struct {

4
pkg/obitax/lca.go
View File

@ -5,8 +5,8 @@ import (
"strconv"
"strings"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
log "github.com/sirupsen/logrus"
)

2
pkg/obitax/sequence_methods.go
View File

@ -1,7 +1,7 @@
package obitax
import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
)
// Setting the taxon at a given rank for a given sequence.

4
pkg/obitax/sequence_predicate.go
View File

@ -3,8 +3,8 @@ package obitax
import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
)
func (taxonomy *Taxonomy) IsAValidTaxon(withAutoCorrection ...bool) obiseq.SequencePredicate {

4
pkg/obitax/sequence_workers.go
View File

@ -1,8 +1,8 @@
package obitax
import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
log "github.com/sirupsen/logrus"
)

94
pkg/obitools/obiannotate/obiannotate.go
View File

@ -1,14 +1,17 @@
package obiannotate
import (
"fmt"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obicorazick"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitax"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obigrep"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiapat"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obicorazick"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obigrep"
)
func DeleteAttributesWorker(toBeDeleted []string) obiseq.SeqWorker {
@ -22,14 +25,69 @@ func DeleteAttributesWorker(toBeDeleted []string) obiseq.SeqWorker {
return f
}
// func MatchPatternWorker(pattern string, errormax int, allowsIndel bool) obiseq.SeqWorker {
// pat, err := obiapat.MakeApatPattern(pattern, errormax, allowsIndel)
// f := func(s *obiseq.BioSequence) *obiseq.BioSequence {
// apats := obiapat.MakeApatSequence(s, false)
// pat.BestMatch(apats, 0)
// return s
// }
// }
func MatchPatternWorker(pattern, name string, errormax int, allowsIndel bool) obiseq.SeqWorker {
pat, err := obiapat.MakeApatPattern(pattern, errormax, allowsIndel)
if err != nil {
log.Fatalf("error in compiling pattern (%s) : %v", pattern, err)
}
cpat, err := pat.ReverseComplement()
if err != nil {
log.Fatalf("error in reverse-complementing pattern (%s) : %v", pattern, err)
}
slot := "pattern"
if name != "pattern" && name != "" {
slot = fmt.Sprintf("%s_pattern", name)
} else {
name = "pattern"
}
slot_match := fmt.Sprintf("%s_match", name)
slot_error := fmt.Sprintf("%s_error", name)
slot_location := fmt.Sprintf("%s_location", name)
f := func(s *obiseq.BioSequence) *obiseq.BioSequence {
apats, err := obiapat.MakeApatSequence(s, false)
if err != nil {
log.Fatalf("error in preparing sequence %s : %v", s.Id(), err)
}
start, end, nerr, matched := pat.BestMatch(apats, 0, s.Len())
if matched {
annot := s.Annotations()
annot[slot] = pattern
match, err := s.Subsequence(start, end, false)
if err != nil {
log.Fatalf("Error in extracting pattern of sequence %s [%d;%d[ : %v",
s.Id(), start, end, err)
}
annot[slot_match] = match.String()
annot[slot_error] = nerr
annot[slot_location] = fmt.Sprintf("%d..%d", start+1, end)
} else {
start, end, nerr, matched := cpat.BestMatch(apats, 0, s.Len())
if matched {
annot := s.Annotations()
annot[slot] = pattern
match, err := s.Subsequence(start, end, false)
if err != nil {
log.Fatalf("Error in extracting pattern of sequence %s [%d;%d[ : %v",
s.Id(), start, end, err)
}
annot[slot_match] = match.ReverseComplement(true).String()
annot[slot_error] = nerr
annot[slot_location] = fmt.Sprintf("complement(%d..%d)", start+1, end)
}
}
return s
}
return f
}
func ToBeKeptAttributesWorker(toBeKept []string) obiseq.SeqWorker {
@ -229,6 +287,14 @@ func CLIAnnotationWorker() obiseq.SeqWorker {
annotator = annotator.ChainWorkers(w)
}
if CLIHasPattern() {
log.Infof("Match pattern %s with %d error", CLIPattern(), CLIPatternError())
w := MatchPatternWorker(CLIPattern(), CLIHasPatternName(),
CLIPatternError(), CLIPatternInDels())
annotator = annotator.ChainWorkers(w)
}
return annotator
}

39
pkg/obitools/obiannotate/options.go
View File

@ -7,8 +7,8 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obigrep"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obigrep"
"github.com/DavidGamba/go-getoptions"
)
@ -24,6 +24,9 @@ var _setSeqLength = false
var _uniqueID = false
var _ahoCorazick = ""
var _pattern = ""
var _pattern_error = 0
var _pattern_indel = false
var _pattern_name = "pattern"
var _lcaSlot = ""
var _lcaError = 0.0
var _setId = ""
@ -52,6 +55,18 @@ func SequenceAnnotationOptionSet(options *getoptions.GetOpt) {
"to the sequence.",
))
options.StringVar(&_pattern_name, "pattern-name", _pattern_name,
options.Description("specify the name to use as prefix for the slots reporting the match"),
)
options.IntVar(&_pattern_error, "pattern-error", _pattern_error,
options.Description("Maximum number of allowed error during pattern matching"),
)
options.BoolVar(&_pattern_indel, "allows-indels", _pattern_indel,
options.Description("Allows for indel during pattern matching"),
)
options.StringVar(&_lcaSlot, "add-lca-in", _lcaSlot,
options.ArgName("SLOT_NAME"),
options.Description("From the taxonomic annotation of the sequence (taxid slot or merged_taxid slot), "+
@ -264,3 +279,23 @@ func CLIHasCut() bool {
return f != 0 && t != 0
}
func CLIPattern() string {
return _pattern
}
func CLIHasPattern() bool {
return _pattern != ""
}
func CLIHasPatternName() string {
return _pattern_name
}
func CLIPatternError() int {
return _pattern_error
}
func CLIPatternInDels() bool {
return _pattern_indel
}

2
pkg/obitools/obiclean/graph.go
View File

@ -12,7 +12,7 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obialign"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obialign"
"github.com/schollz/progressbar/v3"
)

8
pkg/obitools/obiclean/obiclean.go
View File

@ -4,10 +4,10 @@ import (
"fmt"
"os"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
"github.com/schollz/progressbar/v3"
log "github.com/sirupsen/logrus"
)

2
pkg/obitools/obiclean/options.go
View File

@ -1,7 +1,7 @@
package obiclean
import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"github.com/DavidGamba/go-getoptions"
)

10
pkg/obitools/obicleandb/obicleandb.go
View File

@ -3,11 +3,11 @@ package obicleandb
import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obichunk"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obigrep"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obichunk"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obigrep"
)
func ICleanDB(itertator obiiter.IBioSequence) obiiter.IBioSequence {

7
pkg/obitools/obicleandb/options.go
View File

@ -1,12 +1,11 @@
package obicleandb
import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obigrep"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obigrep"
"github.com/DavidGamba/go-getoptions"
)
var _UpdateTaxids = false
func ObicleanDBOptionSet(options *getoptions.GetOpt) {
@ -24,4 +23,4 @@ func OptionSet(options *getoptions.GetOpt) {
func CLIUpdateTaxids() bool {
return _UpdateTaxids
}
}

22
pkg/obitools/obiconsensus/obiconsensus.go
View File

@ -8,11 +8,11 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obikmer"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obisuffix"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obikmer"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obisuffix"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
)
func BuildConsensus(seqs obiseq.BioSequenceSlice,
@ -83,20 +83,20 @@ func BuildConsensus(seqs obiseq.BioSequenceSlice,
}
graph.FilterMin(threshold)
log.Printf("Graph size : %d\n", graph.Len())
if save_graph {
file, err := os.Create(path.Join(dirname,
fmt.Sprintf("%s.gml", seqs[0].Source())))
if err != nil {
fmt.Println(err)
} else {
file.WriteString(graph.Gml())
file.Close()
}
}
}
seq, err := graph.LongestConsensus(seqs[0].Source())
@ -122,11 +122,11 @@ func Consensus(iterator obiiter.IBioSequence) obiiter.IBioSequence {
// path does not exist or is not directory
os.RemoveAll(dirname)
err := os.Mkdir(dirname, 0755)
if err != nil {
log.Panicf("Cannot create directory %s for saving graphs", dirname)
}
}
}
}
newIter.Add(1)

4
pkg/obitools/obiconsensus/options.go
View File

@ -1,7 +1,7 @@
package obiconsensus
import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"github.com/DavidGamba/go-getoptions"
)
@ -66,4 +66,4 @@ func CLIKmerDepth() float64 {
func CLIThreshold() float64 {
return _threshold
}
}

6
pkg/obitools/obiconvert/sequence_reader.go
View File

@ -8,9 +8,9 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
)
func _ExpandListOfFiles(check_ext bool, filenames ...string) ([]string, error) {

6
pkg/obitools/obiconvert/sequence_writer.go
View File

@ -6,9 +6,9 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
)
func BuildPairedFileNames(filename string) (string, string) {

8
pkg/obitools/obicsv/obicsv.go
View File

@ -3,10 +3,10 @@ package obicsv
import (
"log"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
)
func CLIWriteCSV(iterator obiiter.IBioSequence,

4
pkg/obitools/obicsv/options.go
View File

@ -1,8 +1,8 @@
package obicsv
import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
"github.com/DavidGamba/go-getoptions"
)

10
pkg/obitools/obidistribute/distribute.go
View File

@ -3,13 +3,13 @@ package obidistribute
import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
)
func DistributeSequence(sequences obiiter.IBioSequence) {
func CLIDistributeSequence(sequences obiiter.IBioSequence) {
opts := make([]obiformats.WithOption, 0, 10)

9
pkg/obitools/obidistribute/options.go
View File

@ -6,8 +6,8 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"github.com/DavidGamba/go-getoptions"
)
@ -37,7 +37,7 @@ func DistributeOptionSet(options *getoptions.GetOpt) {
options.Alias("d"),
options.Description("The name of a tag annotating the sequences. "+
"The name must corresponds to a string, a integer or a boolean value. "+
"That value will be used to dispatch sequences amoong the different directory " +
"That value will be used to dispatch sequences amoong the different directory "+
"in conjunction with the -c|--classifier options"))
options.StringVar(&_NAValue, "na-value", _NAValue,
@ -66,11 +66,10 @@ func CLIAppendSequences() bool {
return _append
}
func CLISequenceClassifier() *obiseq.BioSequenceClassifier {
switch {
case _SequenceClassifierTag != "":
return obiseq.DualAnnotationClassifier(_SequenceClassifierTag,_DirectoryTag, _NAValue)
return obiseq.DualAnnotationClassifier(_SequenceClassifierTag, _DirectoryTag, _NAValue)
case _BatchCount > 0:
return obiseq.RotateClassifier(_BatchCount)
case _HashSize > 0:

2
pkg/obitools/obifind/iterator.go
View File

@ -4,7 +4,7 @@ import (
"bytes"
"fmt"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitax"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
)
func IFilterRankRestriction() func(*obitax.ITaxonSet) *obitax.ITaxonSet {

4
pkg/obitools/obifind/options.go
View File

@ -3,8 +3,8 @@ package obifind
import (
"errors"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats/ncbitaxdump"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitax"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats/ncbitaxdump"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
"github.com/DavidGamba/go-getoptions"
)

6
pkg/obitools/obigrep/grep.go
View File

@ -3,9 +3,9 @@ package obigrep
import (
"log"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
)
func CLIFilterSequence(iterator obiiter.IBioSequence) obiiter.IBioSequence {

10
pkg/obitools/obigrep/options.go
View File

@ -5,11 +5,11 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats/ncbitaxdump"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitax"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats/ncbitaxdump"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
"github.com/DavidGamba/go-getoptions"
)

11
pkg/obitools/obimatrix/obimatrix.go
View File

@ -2,15 +2,16 @@ package obimatrix
import (
"encoding/csv"
log "github.com/sirupsen/logrus"
"os"
"sort"
"sync"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
"golang.org/x/exp/maps"
)

2
pkg/obitools/obimatrix/options.go
View File

@ -5,7 +5,7 @@
package obimatrix
import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"github.com/DavidGamba/go-getoptions"
)

10
pkg/obitools/obimultiplex/demultiplex.go
View File

@ -3,11 +3,11 @@ package obimultiplex
import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obingslibrary"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obingslibrary"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
)
func IExtractBarcode(iterator obiiter.IBioSequence) (obiiter.IBioSequence, error) {

10
pkg/obitools/obimultiplex/options.go
View File

@ -4,9 +4,9 @@ import (
"fmt"
"os"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obingslibrary"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obingslibrary"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"github.com/DavidGamba/go-getoptions"
)
@ -21,7 +21,7 @@ var _ConservedError = false
// The function adds to a CLI every options proposed to the user
// to tune the parametters of the PCR simulation algorithm.
//
// Parameters
// # Parameters
//
// - option : is a pointer to a getoptions.GetOpt instance normaly
// produced by the
@ -34,7 +34,7 @@ func MultiplexOptionSet(options *getoptions.GetOpt) {
options.BoolVar(&_ConservedError, "keep-errors", _ConservedError,
options.Description("Prints symbol counts."))
options.BoolVar(&_AllowsIndel, "with-indels", _AllowsIndel,
options.BoolVar(&_AllowsIndel, "with-indels", _AllowsIndel,
options.Description("Allows for indels during the primers matching."))
options.StringVar(&_UnidentifiedFile, "unidentified", _UnidentifiedFile,

4
pkg/obitools/obipairing/options.go
View File

@ -1,8 +1,8 @@
package obipairing
import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"github.com/DavidGamba/go-getoptions"
)

8
pkg/obitools/obipairing/pairing.go
View File

@ -5,10 +5,10 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obialign"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obialign"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
)
func _Abs(x int) int {

4
pkg/obitools/obipcr/options.go
View File

@ -5,8 +5,8 @@ package obipcr
import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiapat"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiapat"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"github.com/DavidGamba/go-getoptions"
)

8
pkg/obitools/obipcr/pcr.go
View File

@ -1,10 +1,10 @@
package obipcr
import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiapat"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiapat"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
log "github.com/sirupsen/logrus"
)

6
pkg/obitools/obirefidx/geomindexing.go
View File

@ -6,9 +6,9 @@ import (
"sort"
"sync"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitax"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
)
func GeomIndexSesquence(seqidx int,

16
pkg/obitools/obirefidx/obirefidx.go
View File

@ -6,14 +6,14 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obialign"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obikmer"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitax"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obifind"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obialign"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obikmer"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obifind"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
"github.com/schollz/progressbar/v3"
)

4
pkg/obitools/obirefidx/options.go
View File

@ -1,8 +1,8 @@
package obirefidx
import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obifind"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obifind"
"github.com/DavidGamba/go-getoptions"
)

8
pkg/obitools/obisummary/obisummary.go
View File

@ -3,10 +3,10 @@ package obisummary
import (
"sync"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
)
type DataSummary struct {

2
pkg/obitools/obisummary/options.go
View File

@ -5,7 +5,7 @@
package obisummary
import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"github.com/DavidGamba/go-getoptions"
)

10
pkg/obitools/obitag/obigeomtag.go
View File

@ -4,11 +4,11 @@ import (
"log"
"math"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obialign"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitax"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obialign"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
)
// ExtractLandmarkSeqs extracts landmark sequences from the given BioSequenceSlice.

16
pkg/obitools/obitag/obitag.go
View File

@ -7,14 +7,14 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obialign"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obikmer"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitax"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obirefidx"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obialign"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obikmer"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obirefidx"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
)
// MatchDistanceIndex returns the taxid, rank, and scientificName based on the given distance and distanceIdx.

12
pkg/obitools/obitag/options.go
View File

@ -3,12 +3,12 @@ package obitag
import (
"log"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obifind"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obifind"
"github.com/DavidGamba/go-getoptions"
)

4
pkg/obitools/obitagpcr/options.go
View File

@ -1,8 +1,8 @@
package obitagpcr
import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obimultiplex"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obipairing"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obimultiplex"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obipairing"
"github.com/DavidGamba/go-getoptions"
)

14
pkg/obitools/obitagpcr/pcrtag.go
View File

@ -3,13 +3,13 @@ package obitagpcr
import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obialign"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obimultiplex"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obipairing"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obialign"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obimultiplex"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obipairing"
)
func IPCRTagPESequencesBatch(iterator obiiter.IBioSequence,

2
pkg/obitools/obiuniq/options.go
View File

@ -1,7 +1,7 @@
package obiuniq
import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"github.com/DavidGamba/go-getoptions"
)

6
pkg/obitools/obiuniq/unique.go
View File

@ -3,9 +3,9 @@ package obiuniq
import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obichunk"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obichunk"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
)
func Unique(sequences obiiter.IBioSequence) obiiter.IBioSequence {

457
pkg/obiutils/uint128.go Normal file
View File

@ -0,0 +1,457 @@
package obiutils // import "lukechampine.com/uint128"
// copied from https://github.com/lukechampine/uint128
import (
"encoding/binary"
"errors"
"fmt"
"math"
"math/big"
"math/bits"
)
// Zero is a zero-valued uint128.
var Zero Uint128
// Max is the largest possible uint128 value.
var Max = New(math.MaxUint64, math.MaxUint64)
// A Uint128 is an unsigned 128-bit number.
type Uint128 struct {
Lo, Hi uint64
}
// IsZero returns true if u == 0.
func (u Uint128) IsZero() bool {
// NOTE: we do not compare against Zero, because that is a global variable
// that could be modified.
return u == Uint128{}
}
// Equals returns true if u == v.
//
// Uint128 values can be compared directly with ==, but use of the Equals method
// is preferred for consistency.
func (u Uint128) Equals(v Uint128) bool {
return u == v
}
// Equals64 returns true if u == v.
func (u Uint128) Equals64(v uint64) bool {
return u.Lo == v && u.Hi == 0
}
// Cmp compares u and v and returns:
//
// -1 if u < v
// 0 if u == v
// +1 if u > v
//
func (u Uint128) Cmp(v Uint128) int {
if u == v {
return 0
} else if u.Hi < v.Hi || (u.Hi == v.Hi && u.Lo < v.Lo) {
return -1
} else {
return 1
}
}
// Cmp64 compares u and v and returns:
//
// -1 if u < v
// 0 if u == v
// +1 if u > v
//
func (u Uint128) Cmp64(v uint64) int {
if u.Hi == 0 && u.Lo == v {
return 0
} else if u.Hi == 0 && u.Lo < v {
return -1
} else {
return 1
}
}
// And returns u&v.
func (u Uint128) And(v Uint128) Uint128 {
return Uint128{u.Lo & v.Lo, u.Hi & v.Hi}
}
// And64 returns u&v.
func (u Uint128) And64(v uint64) Uint128 {
return Uint128{u.Lo & v, u.Hi & 0}
}
// Or returns u|v.
func (u Uint128) Or(v Uint128) Uint128 {
return Uint128{u.Lo | v.Lo, u.Hi | v.Hi}
}
// Or64 returns u|v.
func (u Uint128) Or64(v uint64) Uint128 {
return Uint128{u.Lo | v, u.Hi | 0}
}
// Xor returns u^v.
func (u Uint128) Xor(v Uint128) Uint128 {
return Uint128{u.Lo ^ v.Lo, u.Hi ^ v.Hi}
}
// Xor64 returns u^v.
func (u Uint128) Xor64(v uint64) Uint128 {
return Uint128{u.Lo ^ v, u.Hi ^ 0}
}
// Add returns u+v.
func (u Uint128) Add(v Uint128) Uint128 {
lo, carry := bits.Add64(u.Lo, v.Lo, 0)
hi, carry := bits.Add64(u.Hi, v.Hi, carry)
if carry != 0 {
panic("overflow")
}
return Uint128{lo, hi}
}
// AddWrap returns u+v with wraparound semantics; for example,
// Max.AddWrap(From64(1)) == Zero.
func (u Uint128) AddWrap(v Uint128) Uint128 {
lo, carry := bits.Add64(u.Lo, v.Lo, 0)
hi, _ := bits.Add64(u.Hi, v.Hi, carry)
return Uint128{lo, hi}
}
// Add64 returns u+v.
func (u Uint128) Add64(v uint64) Uint128 {
lo, carry := bits.Add64(u.Lo, v, 0)
hi, carry := bits.Add64(u.Hi, 0, carry)
if carry != 0 {
panic("overflow")
}
return Uint128{lo, hi}
}
// AddWrap64 returns u+v with wraparound semantics; for example,
// Max.AddWrap64(1) == Zero.
func (u Uint128) AddWrap64(v uint64) Uint128 {
lo, carry := bits.Add64(u.Lo, v, 0)
hi := u.Hi + carry
return Uint128{lo, hi}
}
// Sub returns u-v.
func (u Uint128) Sub(v Uint128) Uint128 {
lo, borrow := bits.Sub64(u.Lo, v.Lo, 0)
hi, borrow := bits.Sub64(u.Hi, v.Hi, borrow)
if borrow != 0 {
panic("underflow")
}
return Uint128{lo, hi}
}
// SubWrap returns u-v with wraparound semantics; for example,
// Zero.SubWrap(From64(1)) == Max.
func (u Uint128) SubWrap(v Uint128) Uint128 {
lo, borrow := bits.Sub64(u.Lo, v.Lo, 0)
hi, _ := bits.Sub64(u.Hi, v.Hi, borrow)
return Uint128{lo, hi}
}
// Sub64 returns u-v.
func (u Uint128) Sub64(v uint64) Uint128 {
lo, borrow := bits.Sub64(u.Lo, v, 0)
hi, borrow := bits.Sub64(u.Hi, 0, borrow)
if borrow != 0 {
panic("underflow")
}
return Uint128{lo, hi}
}
// SubWrap64 returns u-v with wraparound semantics; for example,
// Zero.SubWrap64(1) == Max.
func (u Uint128) SubWrap64(v uint64) Uint128 {
lo, borrow := bits.Sub64(u.Lo, v, 0)
hi := u.Hi - borrow
return Uint128{lo, hi}
}
// Mul returns u*v, panicking on overflow.
func (u Uint128) Mul(v Uint128) Uint128 {
hi, lo := bits.Mul64(u.Lo, v.Lo)
p0, p1 := bits.Mul64(u.Hi, v.Lo)
p2, p3 := bits.Mul64(u.Lo, v.Hi)
hi, c0 := bits.Add64(hi, p1, 0)
hi, c1 := bits.Add64(hi, p3, c0)
if (u.Hi != 0 && v.Hi != 0) || p0 != 0 || p2 != 0 || c1 != 0 {
panic("overflow")
}
return Uint128{lo, hi}
}
// MulWrap returns u*v with wraparound semantics; for example,
// Max.MulWrap(Max) == 1.
func (u Uint128) MulWrap(v Uint128) Uint128 {
hi, lo := bits.Mul64(u.Lo, v.Lo)
hi += u.Hi*v.Lo + u.Lo*v.Hi
return Uint128{lo, hi}
}
// Mul64 returns u*v, panicking on overflow.
func (u Uint128) Mul64(v uint64) Uint128 {
hi, lo := bits.Mul64(u.Lo, v)
p0, p1 := bits.Mul64(u.Hi, v)
hi, c0 := bits.Add64(hi, p1, 0)
if p0 != 0 || c0 != 0 {
panic("overflow")
}
return Uint128{lo, hi}
}
// MulWrap64 returns u*v with wraparound semantics; for example,
// Max.MulWrap64(2) == Max.Sub64(1).
func (u Uint128) MulWrap64(v uint64) Uint128 {
hi, lo := bits.Mul64(u.Lo, v)
hi += u.Hi * v
return Uint128{lo, hi}
}
// Div returns u/v.
func (u Uint128) Div(v Uint128) Uint128 {
q, _ := u.QuoRem(v)
return q
}
// Div64 returns u/v.
func (u Uint128) Div64(v uint64) Uint128 {
q, _ := u.QuoRem64(v)
return q
}
// QuoRem returns q = u/v and r = u%v.
func (u Uint128) QuoRem(v Uint128) (q, r Uint128) {
if v.Hi == 0 {
var r64 uint64
q, r64 = u.QuoRem64(v.Lo)
r = From64(r64)
} else {
// generate a "trial quotient," guaranteed to be within 1 of the actual
// quotient, then adjust.
n := uint(bits.LeadingZeros64(v.Hi))
v1 := v.Lsh(n)
u1 := u.Rsh(1)
tq, _ := bits.Div64(u1.Hi, u1.Lo, v1.Hi)
tq >>= 63 - n
if tq != 0 {
tq--
}
q = From64(tq)
// calculate remainder using trial quotient, then adjust if remainder is
// greater than divisor
r = u.Sub(v.Mul64(tq))
if r.Cmp(v) >= 0 {
q = q.Add64(1)
r = r.Sub(v)
}
}
return
}
// QuoRem64 returns q = u/v and r = u%v.
func (u Uint128) QuoRem64(v uint64) (q Uint128, r uint64) {
if u.Hi < v {
q.Lo, r = bits.Div64(u.Hi, u.Lo, v)
} else {
q.Hi, r = bits.Div64(0, u.Hi, v)
q.Lo, r = bits.Div64(r, u.Lo, v)
}
return
}
// Mod returns r = u%v.
func (u Uint128) Mod(v Uint128) (r Uint128) {
_, r = u.QuoRem(v)
return
}
// Mod64 returns r = u%v.
func (u Uint128) Mod64(v uint64) (r uint64) {
_, r = u.QuoRem64(v)
return
}
// Lsh returns u<<n.
func (u Uint128) Lsh(n uint) (s Uint128) {
if n > 64 {
s.Lo = 0
s.Hi = u.Lo << (n - 64)
} else {
s.Lo = u.Lo << n
s.Hi = u.Hi<<n | u.Lo>>(64-n)
}
return
}
// Rsh returns u>>n.
func (u Uint128) Rsh(n uint) (s Uint128) {
if n > 64 {
s.Lo = u.Hi >> (n - 64)
s.Hi = 0
} else {
s.Lo = u.Lo>>n | u.Hi<<(64-n)
s.Hi = u.Hi >> n
}
return
}
// LeadingZeros returns the number of leading zero bits in u; the result is 128
// for u == 0.
func (u Uint128) LeadingZeros() int {
if u.Hi > 0 {
return bits.LeadingZeros64(u.Hi)
}
return 64 + bits.LeadingZeros64(u.Lo)
}
// TrailingZeros returns the number of trailing zero bits in u; the result is
// 128 for u == 0.
func (u Uint128) TrailingZeros() int {
if u.Lo > 0 {
return bits.TrailingZeros64(u.Lo)
}
return 64 + bits.TrailingZeros64(u.Hi)
}
// OnesCount returns the number of one bits ("population count") in u.
func (u Uint128) OnesCount() int {
return bits.OnesCount64(u.Hi) + bits.OnesCount64(u.Lo)
}
// RotateLeft returns the value of u rotated left by (k mod 128) bits.
func (u Uint128) RotateLeft(k int) Uint128 {
const n = 128
s := uint(k) & (n - 1)
return u.Lsh(s).Or(u.Rsh(n - s))
}
// RotateRight returns the value of u rotated left by (k mod 128) bits.
func (u Uint128) RotateRight(k int) Uint128 {
return u.RotateLeft(-k)
}
// Reverse returns the value of u with its bits in reversed order.
func (u Uint128) Reverse() Uint128 {
return Uint128{bits.Reverse64(u.Hi), bits.Reverse64(u.Lo)}
}
// ReverseBytes returns the value of u with its bytes in reversed order.
func (u Uint128) ReverseBytes() Uint128 {
return Uint128{bits.ReverseBytes64(u.Hi), bits.ReverseBytes64(u.Lo)}
}
// Len returns the minimum number of bits required to represent u; the result is
// 0 for u == 0.
func (u Uint128) Len() int {
return 128 - u.LeadingZeros()
}
// String returns the base-10 representation of u as a string.
func (u Uint128) String() string {
if u.IsZero() {
return "0"
}
buf := []byte("0000000000000000000000000000000000000000") // log10(2^128) < 40
for i := len(buf); ; i -= 19 {
q, r := u.QuoRem64(1e19) // largest power of 10 that fits in a uint64
var n int
for ; r != 0; r /= 10 {
n++
buf[i-n] += byte(r % 10)
}
if q.IsZero() {
return string(buf[i-n:])
}
u = q
}
}
// PutBytes stores u in b in little-endian order. It panics if len(b) < 16.
func (u Uint128) PutBytes(b []byte) {
binary.LittleEndian.PutUint64(b[:8], u.Lo)
binary.LittleEndian.PutUint64(b[8:], u.Hi)
}
// PutBytesBE stores u in b in big-endian order. It panics if len(ip) < 16.
func (u Uint128) PutBytesBE(b []byte) {
binary.BigEndian.PutUint64(b[:8], u.Hi)
binary.BigEndian.PutUint64(b[8:], u.Lo)
}
// Big returns u as a *big.Int.
func (u Uint128) Big() *big.Int {
i := new(big.Int).SetUint64(u.Hi)
i = i.Lsh(i, 64)
i = i.Xor(i, new(big.Int).SetUint64(u.Lo))
return i
}
// Scan implements fmt.Scanner.
func (u *Uint128) Scan(s fmt.ScanState, ch rune) error {
i := new(big.Int)
if err := i.Scan(s, ch); err != nil {
return err
} else if i.Sign() < 0 {
return errors.New("value cannot be negative")
} else if i.BitLen() > 128 {
return errors.New("value overflows Uint128")
}
u.Lo = i.Uint64()
u.Hi = i.Rsh(i, 64).Uint64()
return nil
}
// New returns the Uint128 value (lo,hi).
func New(lo, hi uint64) Uint128 {
return Uint128{lo, hi}
}
// From64 converts v to a Uint128 value.
func From64(v uint64) Uint128 {
return New(v, 0)
}
// FromBytes converts b to a Uint128 value.
func FromBytes(b []byte) Uint128 {
return New(
binary.LittleEndian.Uint64(b[:8]),
binary.LittleEndian.Uint64(b[8:]),
)
}
// FromBytesBE converts big-endian b to a Uint128 value.
func FromBytesBE(b []byte) Uint128 {
return New(
binary.BigEndian.Uint64(b[8:]),
binary.BigEndian.Uint64(b[:8]),
)
}
// FromBig converts i to a Uint128 value. It panics if i is negative or
// overflows 128 bits.
func FromBig(i *big.Int) (u Uint128) {
if i.Sign() < 0 {
panic("value cannot be negative")
} else if i.BitLen() > 128 {
panic("value overflows Uint128")
}
u.Lo = i.Uint64()
u.Hi = i.Rsh(i, 64).Uint64()
return u
}
// FromString parses s as a Uint128 value.
func FromString(s string) (u Uint128, err error) {
_, err = fmt.Sscan(s, &u)
return
}