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Patch module name from oa2 to obitools

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This commit is contained in:
Eric Coissac
2022-01-13 23:43:01 +01:00
parent f53bf1b804
commit b9b9c0f179
47 changed files with 82 additions and 401 deletions
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4
.gitignore vendored Normal file
View File

@ -0,0 +1,4 @@
cpu.pprof
cpu.trace
obicount
obipairing

4
cmd/obitools/obiconvert/main.go
View File

@ -3,9 +3,9 @@ package main
import (
"os"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obitools/obiconvert"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
)
func main() {

6
cmd/obitools/obicount/main.go
View File

@ -6,10 +6,10 @@ import (
"os"
"runtime/trace"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obitools/obiconvert"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obitools/obicount"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obicount"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
)
func main() {

4
cmd/obitools/obifind/main.go
View File

@ -4,8 +4,8 @@ import (
"fmt"
"os"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obitools/obifind"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obifind"
)
func main() {

6
cmd/obitools/obipairing/main.go
View File

@ -5,9 +5,9 @@ import (
"os"
"runtime/pprof"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiformats"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obitools/obipairing"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obipairing"
)
func main() {

6
cmd/obitools/obipcr/main.go
View File

@ -3,9 +3,9 @@ package main
import (
"os"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obitools/obiconvert"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obitools/obipcr"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obipcr"
)
func main() {

4
cmd/test/main.go
View File

@ -6,8 +6,8 @@ import (
"os"
"runtime/trace"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obialign"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obialign"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
func main() {

6
cmd/test/test_test.go
View File

@ -4,9 +4,9 @@ import (
"fmt"
"testing"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiannot"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiformats"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiannot"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
func TestParseOBIFasta(t *testing.T) {

15
go.mod Normal file
View File

@ -0,0 +1,15 @@
module git.metabarcoding.org/lecasofts/go/obitools
go 1.17
require (
github.com/DavidGamba/go-getoptions v0.25.0 // indirect
github.com/goccy/go-json v0.9.1 // indirect
github.com/mattn/go-runewidth v0.0.13 // indirect
github.com/mitchellh/colorstring v0.0.0-20190213212951-d06e56a500db // indirect
github.com/rivo/uniseg v0.2.0 // indirect
github.com/schollz/progressbar/v3 v3.8.5 // indirect
golang.org/x/crypto v0.0.0-20211215153901-e495a2d5b3d3 // indirect
golang.org/x/sys v0.0.0-20211216021012-1d35b9e2eb4e // indirect
golang.org/x/term v0.0.0-20210927222741-03fcf44c2211 // indirect
)

5
go.sum
View File

@ -57,6 +57,8 @@ github.com/BurntSushi/xgb v0.0.0-20160522181843-27f122750802/go.mod h1:IVnqGOEym
github.com/DATA-DOG/go-sqlmock v1.3.3/go.mod h1:f/Ixk793poVmq4qj/V1dPUg2JEAKC73Q5eFN3EC/SaM=
github.com/DavidGamba/go-getoptions v0.24.0 h1:Nz9lUWRjzxdkC4YRU5UaqiHZS0uA/Ak9b9FCfD1AlUM=
github.com/DavidGamba/go-getoptions v0.24.0/go.mod h1:qLaLSYeQ8sUVOfKuu5JT5qKKS3OCwyhkYSJnoG+ggmo=
github.com/DavidGamba/go-getoptions v0.25.0 h1:lc66nzD7BPN9RtNN6us8FWFFUjKi7C4+EF8MPMj+I9U=
github.com/DavidGamba/go-getoptions v0.25.0/go.mod h1:qLaLSYeQ8sUVOfKuu5JT5qKKS3OCwyhkYSJnoG+ggmo=
github.com/Djarvur/go-err113 v0.0.0-20210108212216-aea10b59be24/go.mod h1:4UJr5HIiMZrwgkSPdsjy2uOQExX/WEILpIrO9UPGuXs=
github.com/Masterminds/goutils v1.1.0/go.mod h1:8cTjp+g8YejhMuvIA5y2vz3BpJxksy863GQaJW2MFNU=
github.com/Masterminds/semver v1.4.2/go.mod h1:MB6lktGJrhw8PrUyiEoblNEGEQ+RzHPF078ddwwvV3Y=
@ -198,6 +200,8 @@ github.com/go-xmlfmt/xmlfmt v0.0.0-20191208150333-d5b6f63a941b/go.mod h1:aUCEOzz
github.com/gobwas/glob v0.2.3/go.mod h1:d3Ez4x06l9bZtSvzIay5+Yzi0fmZzPgnTbPcKjJAkT8=
github.com/goccy/go-json v0.7.10 h1:ulhbuNe1JqE68nMRXXTJRrUu0uhouf0VevLINxQq4Ec=
github.com/goccy/go-json v0.7.10/go.mod h1:6MelG93GURQebXPDq3khkgXZkazVtN9CRI+MGFi0w8I=
github.com/goccy/go-json v0.9.1 h1:xurvfvj3gq6SWUkkZ0opoUDTms7jif41uZ9z9s+hVlY=
github.com/goccy/go-json v0.9.1/go.mod h1:6MelG93GURQebXPDq3khkgXZkazVtN9CRI+MGFi0w8I=
github.com/godbus/dbus/v5 v5.0.4/go.mod h1:xhWf0FNVPg57R7Z0UbKHbJfkEywrmjJnf7w5xrFpKfA=
github.com/gofrs/flock v0.8.1/go.mod h1:F1TvTiK9OcQqauNUHlbJvyl9Qa1QvF/gOUDKA14jxHU=
github.com/gogo/protobuf v1.1.1/go.mod h1:r8qH/GZQm5c6nD/R0oafs1akxWv10x8SbQlK7atdtwQ=
@ -912,6 +916,7 @@ golang.org/x/sys v0.0.0-20210927094055-39ccf1dd6fa6/go.mod h1:oPkhp1MJrh7nUepCBc
golang.org/x/sys v0.0.0-20211013075003-97ac67df715c/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
golang.org/x/sys v0.0.0-20211124211545-fe61309f8881 h1:TyHqChC80pFkXWraUUf6RuB5IqFdQieMLwwCJokV2pc=
golang.org/x/sys v0.0.0-20211124211545-fe61309f8881/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
golang.org/x/sys v0.0.0-20211216021012-1d35b9e2eb4e h1:fLOSk5Q00efkSvAm+4xcoXD+RRmLmmulPn5I3Y9F2EM=
golang.org/x/sys v0.0.0-20211216021012-1d35b9e2eb4e/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
golang.org/x/sys v0.0.0-20220111092808-5a964db01320 h1:0jf+tOCoZ3LyutmCOWpVni1chK4VfFLhRsDK7MhqGRY=
golang.org/x/sys v0.0.0-20220111092808-5a964db01320/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=

18
obitools/obiconvert/main.go
View File

@ -1,18 +0,0 @@
package main
import (
"os"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obitools/obiconvert"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obioptions"
)
func main() {
option_parser := obioptions.GenerateOptionParser(obiconvert.OptionSet)
_, args, _ := option_parser(os.Args)
fs, _ := obiconvert.ReadBioSequences(args...)
obiconvert.WriteBioSequences(fs)
}

65
obitools/obicount/main.go
View File

@ -1,65 +0,0 @@
package main
import (
"fmt"
"log"
"os"
"runtime/trace"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obitools/obiconvert"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obitools/obicount"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obioptions"
)
func main() {
// f, err := os.Create("cpu.pprof")
// if err != nil {
// log.Fatal(err)
// }
// pprof.StartCPUProfile(f)
// defer pprof.StopCPUProfile()
ftrace, err := os.Create("cpu.trace")
if err != nil {
log.Fatal(err)
}
trace.Start(ftrace)
defer trace.Stop()
option_parser := obioptions.GenerateOptionParser(
obiconvert.InputOptionSet,
obicount.OptionSet,
)
_, args, _ := option_parser(os.Args)
fs, _ := obiconvert.ReadBioSequences(args...)
nread := 0
nvariant := 0
nsymbol := 0
for fs.Next() {
s := fs.Get()
if s.IsNil() {
log.Panicln("Read sequence is nil")
}
nread += s.Count()
nvariant++
nsymbol += s.Length()
}
if obicount.IsPrintingVariantCount() {
fmt.Printf(" %d", nvariant)
}
if obicount.IsPrintingReadCount() {
fmt.Printf(" %d", nread)
}
if obicount.IsPrintingSymbolCount() {
fmt.Printf(" %d", nsymbol)
}
fmt.Printf("\n")
}

68
obitools/obifind/main.go
View File

@ -1,68 +0,0 @@
package main
import (
"fmt"
"os"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obitools/obifind"
)
func main() {
option_parser := obioptions.GenerateOptionParser(obifind.OptionSet)
_, args, _ := option_parser(os.Args)
//prof, _ := os.Create("obifind.prof")
//pprof.StartCPUProfile(prof)
restrictions, err := obifind.ITaxonRestrictions()
if err != nil {
fmt.Printf("%+v", err)
}
switch {
case obifind.RequestsPathForTaxid() >= 0:
taxonomy, err := obifind.LoadSelectedTaxonomy()
if err != nil {
fmt.Printf("%+v", err)
}
taxon, err := taxonomy.Taxon(obifind.RequestsPathForTaxid())
if err != nil {
fmt.Printf("%+v", err)
}
s, err := taxon.Path()
if err != nil {
fmt.Printf("%+v", err)
}
obifind.TaxonWriter(s.Iterator(),
fmt.Sprintf("path:%d", taxon.Taxid()))
case len(args) == 0:
taxonomy, err := obifind.LoadSelectedTaxonomy()
if err != nil {
fmt.Printf("%+v", err)
}
obifind.TaxonWriter(restrictions(taxonomy.Iterator()), "")
default:
matcher, err := obifind.ITaxonNameMatcher()
if err != nil {
fmt.Printf("%+v", err)
}
for _, pattern := range args {
s := restrictions(matcher(pattern))
obifind.TaxonWriter(s, pattern)
}
}
//pprof.StopCPUProfile()
}

38
obitools/obipairing/main.go
View File

@ -1,38 +0,0 @@
package main
import (
"log"
"os"
"runtime/pprof"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiformats"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obitools/obipairing"
)
func main() {
// go tool pprof -http=":8000" ./obipairing ./cpu.pprof
f, err := os.Create("cpu.pprof")
if err != nil {
log.Fatal(err)
}
pprof.StartCPUProfile(f)
defer pprof.StopCPUProfile()
// go tool trace cpu.trace
// ftrace, err := os.Create("cpu.trace")
// if err != nil {
// log.Fatal(err)
// }
// trace.Start(ftrace)
// defer trace.Stop()
option_parser := obioptions.GenerateOptionParser(obipairing.OptionSet)
option_parser(os.Args)
pairs, _ := obipairing.IBatchPairedSequence()
paired := obipairing.IAssemblePESequencesBatch(pairs, 2, 50, 20, true)
written, _ := obiformats.WriteFastqBatchToStdout(paired)
written.Destroy()
}

34
obitools/obipcr/main.go
View File

@ -1,34 +0,0 @@
package main
import (
"os"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obitools/obiconvert"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obitools/obipcr"
)
func main() {
// f, err := os.Create("cpu.pprof")
// if err != nil {
// log.Fatal(err)
// }
// pprof.StartCPUProfile(f)
// defer pprof.StopCPUProfile()
// ftrace, err := os.Create("cpu.trace")
// if err != nil {
// log.Fatal(err)
// }
// trace.Start(ftrace)
// defer trace.Stop()
option_parser := obioptions.GenerateOptionParser(obipcr.OptionSet)
_, args, _ := option_parser(os.Args)
sequences, _ := obiconvert.ReadBioSequencesBatch(args...)
amplicons, _ := obipcr.PCR(sequences)
obiconvert.WriteBioSequences(amplicons)
}

2
pkg/obialign/alignment.go
View File

@ -3,7 +3,7 @@ package obialign
import (
"math"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
type __build_align_arena__ struct {

2
pkg/obialign/fourbitsencode.go
View File

@ -1,7 +1,7 @@
package obialign
import (
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
var __four_bits_base_code__ = []byte{0b0000,

4
pkg/obialign/pairedendalign.go
View File

@ -3,8 +3,8 @@ package obialign
import (
"log"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obikmer"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obikmer"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
type __pe_align_arena__ struct {

2
pkg/obiapat/pattern.go
View File

@ -10,7 +10,7 @@ import (
"errors"
"unsafe"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
var MAX_PAT_LEN = int(C.MAX_PAT_LEN)

4
pkg/obiapat/pcr.go
View File

@ -1,8 +1,8 @@
package obiapat
import (
"git.metabarcoding.org/lecasofts/go/oa2/pkg/goutils"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
type __options__ struct {

2
pkg/obiformats/ecopcr_read.go
View File

@ -10,7 +10,7 @@ import (
"strconv"
"strings"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
type __ecopcr_file__ struct {

2
pkg/obiformats/embl_read.go
View File

@ -11,7 +11,7 @@ import (
"strings"
"time"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
var __FILE_CHUNK_SIZE__ = 1 << 20

2
pkg/obiformats/fastseq_header.go
View File

@ -3,7 +3,7 @@ package obiformats
import (
"strings"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
func ParseGuessedFastSeqHeader(sequence obiseq.BioSequence) {

2
pkg/obiformats/fastseq_interface.go
View File

@ -1,5 +1,5 @@
package obiformats
import "git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
import "git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
type FormatHeader func(sequence obiseq.BioSequence) string

2
pkg/obiformats/fastseq_json_header.go
View File

@ -3,7 +3,7 @@ package obiformats
import (
"strings"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"github.com/goccy/go-json"
)

2
pkg/obiformats/fastseq_obi_header.go
View File

@ -7,7 +7,7 @@ import (
"strconv"
"strings"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"github.com/goccy/go-json"
)

4
pkg/obiformats/fastseq_read.go
View File

@ -14,8 +14,8 @@ import (
"time"
"unsafe"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/cutils"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/cutils"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
func __fastseq_reader__(seqfile C.fast_kseq_p,

2
pkg/obiformats/fastseq_write_fasta.go
View File

@ -10,7 +10,7 @@ import (
"sync"
"time"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
func min(x, y int) int {

2
pkg/obiformats/fastseq_write_fastq.go
View File

@ -8,7 +8,7 @@ import (
"os"
"time"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
func FormatFastq(seq obiseq.BioSequence, quality_shift int, formater FormatHeader) string {

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

@ -12,7 +12,7 @@ import (
"strconv"
"strings"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obitax"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitax"
)
func loadNodeTable(reader io.Reader, taxonomy *obitax.Taxonomy) {

2
pkg/obiformats/options.go
View File

@ -1,6 +1,6 @@
package obiformats
import "git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
import "git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
type __options__ struct {
fastseq_header_parser obiseq.SeqAnnotator

2
pkg/obiformats/universal_read.go
View File

@ -8,7 +8,7 @@ import (
"os"
"strings"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
func GuessSeqFileType(firstline string) string {

2
pkg/obiformats/universal_write.go
View File

@ -6,7 +6,7 @@ import (
"log"
"os"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
func WriteSequences(iterator obiseq.IBioSequence,

2
pkg/obikmer/encodefourmer.go
View File

@ -1,6 +1,6 @@
package obikmer
import "git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
import "git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
var __single_base_code__ = []byte{0,
// A, B, C, D,

2
pkg/obiseq/biosequence.go
View File

@ -4,7 +4,7 @@ import (
"bytes"
"crypto/md5"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/goutils"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
)
type Quality []uint8

2
pkg/obiseq/join.go
View File

@ -1,6 +1,6 @@
package obiseq
import "git.metabarcoding.org/lecasofts/go/oa2/pkg/goutils"
import "git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
func (sequence BioSequence) Join(seq2 BioSequence, copy_annot bool) (BioSequence, error) {

2
pkg/obiseq/subseq.go
View File

@ -4,7 +4,7 @@ import (
"errors"
"fmt"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/goutils"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
)
// Returns a sub sequence start from position 'from' included,

4
pkg/obitools/obiconvert/sequence_reader.go
View File

@ -6,8 +6,8 @@ import (
"path/filepath"
"strings"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiformats"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
func __expand_list_of_files__(check_ext bool, filenames ...string) ([]string, error) {

4
pkg/obitools/obiconvert/sequence_writer.go
View File

@ -3,8 +3,8 @@ package obiconvert
import (
"log"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiformats"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
func WriteBioSequences(iterator obiseq.IBioSequence, filenames ...string) error {

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

@ -4,7 +4,7 @@ import (
"bytes"
"fmt"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obitax"
"git.metabarcoding.org/lecasofts/go/obitools/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/oa2/pkg/obiformats/ncbitaxdump"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obitax"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats/ncbitaxdump"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitax"
"github.com/DavidGamba/go-getoptions"
)

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

@ -1,8 +1,8 @@
package obipairing
import (
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obitools/obiconvert"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"github.com/DavidGamba/go-getoptions"
)

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

@ -6,8 +6,8 @@ import (
"os"
"time"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obialign"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obialign"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"github.com/schollz/progressbar/v3"
)

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

@ -3,8 +3,8 @@ package obipcr
import (
"log"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiapat"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obitools/obiconvert"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiapat"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"github.com/DavidGamba/go-getoptions"
)

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

@ -1,8 +1,8 @@
package obipcr
import (
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiapat"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiapat"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
func PCR(iterator obiseq.IBioSequenceBatch) (obiseq.IBioSequence, error) {

62
test/main.go
View File

@ -1,62 +0,0 @@
package main
import (
"fmt"
"log"
"os"
"runtime/trace"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obialign"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
)
func main() {
ftrace, err := os.Create("cpu.trace")
if err != nil {
log.Fatal(err)
}
trace.Start(ftrace)
defer trace.Stop()
// option_parser := obioptions.GenerateOptionParser(
// obiconvert.InputOptionSet,
// )
//_, args, _ := option_parser(os.Args)
// fs, _ := obiconvert.ReadBioSequences(args...)
// buffer := make([]byte, 0)
// fs.Next()
// s := fs.Get()
// index := obikmer.Index4mer(s, nil, nil)
// for fs.Next() {
// s := fs.Get()
// if s.IsNil() {
// log.Panicln("Read sequence is nil")
// }
// maxshift, maxcount := obikmer.FastShiftFourMer(index, s, buffer)
// fmt.Printf("Shift : %d Score : %d\n", maxshift, maxcount)
// }
A := []byte("ccgcctccttagaacaggctcctctagaaaaccatagtgggatatctaaagaaggcggagatagaaagagcggttcagcaggaatgccgagatggacggcgtgtgacg")
B := []byte("cgccaccaccgagatctacactctttccctacacgacgctcttccgatctccgcctccttagaacaggctcctctagaaaagcatagtggggtatctaaaggaggcgg")
sA := obiseq.MakeBioSequence("A", A, "")
sB := obiseq.MakeBioSequence("B", B, "")
fmt.Println(string(sA.Sequence()))
fmt.Println(sA.Qualities())
fmt.Println(string(sB.Sequence()))
fmt.Println(sB.Qualities())
score, path := obialign.PELeftAlign(sA, sB, 2, obialign.NilPEAlignArena)
fmt.Printf("Score : %d Path : %v\n", score, path)
score, path = obialign.PERightAlign(sA, sB, 2, obialign.NilPEAlignArena)
fmt.Printf("Score : %d Path : %v\n", score, path)
fmt.Println(string(sA.Sequence()))
sA.ReverseComplement(true)
fmt.Println(string(sA.Sequence()))
fmt.Println(string(sA.Id()))
}

58
test/test_test.go
View File

@ -1,58 +0,0 @@
package main_test
import (
"fmt"
"testing"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiannot"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiformats"
"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
)
func TestParseOBIFasta(t *testing.T) {
f := "/Users/coissac/travail/Adeline/Soumission_data/Zonation/euka03/euka03.ecotag.fasta.gz"
var nseq, nread int
nseq = 0
nread = 0
fs := obiformats.ReaderFromIlluminaFile(f)
fmt.Println(f)
for i := range obiannot.ExtractHeaderChannel(fs, fastseq.ParseOBIHeader) {
for _, s := range i {
nseq++
nread += s.Count()
}
}
fmt.Println(nseq, nread)
}
func ExtractHeaderChannel(fs fastseq.IFastSeq, sequence func(sequence obiseq.Sequence)) {
panic("unimplemented")
}
// Performance test of an ADEXP message parsing
func BenchmarkParseOBIFasta(t *testing.B) {
f := "/Users/coissac/travail/Adeline/Soumission_data/Zonation/euka03/euka03.ecotag.fasta.gz"
var nseq, nread int
nseq = 0
nread = 0
fs := fastseq.ReaderFromIlluminaFile(f)
fmt.Println(f)
for i := range obiannot.ExtractHeaderChannel(fs, fastseq.ParseOBIHeader) {
for _, s := range i {
nseq++
nread += s.Count()
}
}
fmt.Println(nseq, nread)
}