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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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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 {