diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..093ffcc --- /dev/null +++ b/.gitignore @@ -0,0 +1,4 @@ +cpu.pprof +cpu.trace +obicount +obipairing diff --git a/cmd/obitools/obiconvert/main.go b/cmd/obitools/obiconvert/main.go index 1a15cdb..8dab176 100644 --- a/cmd/obitools/obiconvert/main.go +++ b/cmd/obitools/obiconvert/main.go @@ -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() { diff --git a/cmd/obitools/obicount/main.go b/cmd/obitools/obicount/main.go index a3f7a9d..43876b5 100644 --- a/cmd/obitools/obicount/main.go +++ b/cmd/obitools/obicount/main.go @@ -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() { diff --git a/cmd/obitools/obifind/main.go b/cmd/obitools/obifind/main.go index 3d25313..87ff582 100644 --- a/cmd/obitools/obifind/main.go +++ b/cmd/obitools/obifind/main.go @@ -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() { diff --git a/cmd/obitools/obipairing/main.go b/cmd/obitools/obipairing/main.go index 7b212d2..0644c05 100644 --- a/cmd/obitools/obipairing/main.go +++ b/cmd/obitools/obipairing/main.go @@ -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() { diff --git a/cmd/obitools/obipcr/main.go b/cmd/obitools/obipcr/main.go index 0aafcb5..29f3c75 100644 --- a/cmd/obitools/obipcr/main.go +++ b/cmd/obitools/obipcr/main.go @@ -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() { diff --git a/cmd/test/main.go b/cmd/test/main.go index 5d895a8..6271107 100644 --- a/cmd/test/main.go +++ b/cmd/test/main.go @@ -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() { diff --git a/cmd/test/test_test.go b/cmd/test/test_test.go index 4008ad7..c076ee8 100644 --- a/cmd/test/test_test.go +++ b/cmd/test/test_test.go @@ -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) { diff --git a/go.mod b/go.mod new file mode 100644 index 0000000..317b23d --- /dev/null +++ b/go.mod @@ -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 +) diff --git a/go.sum b/go.sum index 5b02b81..ee623c8 100644 --- a/go.sum +++ b/go.sum @@ -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= diff --git a/obitools/obiconvert/main.go b/obitools/obiconvert/main.go deleted file mode 100644 index 1a15cdb..0000000 --- a/obitools/obiconvert/main.go +++ /dev/null @@ -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) -} diff --git a/obitools/obicount/main.go b/obitools/obicount/main.go deleted file mode 100644 index a3f7a9d..0000000 --- a/obitools/obicount/main.go +++ /dev/null @@ -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") -} diff --git a/obitools/obifind/main.go b/obitools/obifind/main.go deleted file mode 100644 index 3d25313..0000000 --- a/obitools/obifind/main.go +++ /dev/null @@ -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() -} diff --git a/obitools/obipairing/main.go b/obitools/obipairing/main.go deleted file mode 100644 index 7b212d2..0000000 --- a/obitools/obipairing/main.go +++ /dev/null @@ -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() -} diff --git a/obitools/obipcr/main.go b/obitools/obipcr/main.go deleted file mode 100644 index 0aafcb5..0000000 --- a/obitools/obipcr/main.go +++ /dev/null @@ -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) -} diff --git a/pkg/obialign/alignment.go b/pkg/obialign/alignment.go index 86aaf49..e24b10e 100644 --- a/pkg/obialign/alignment.go +++ b/pkg/obialign/alignment.go @@ -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 { diff --git a/pkg/obialign/fourbitsencode.go b/pkg/obialign/fourbitsencode.go index 401de1d..ca2b4f5 100644 --- a/pkg/obialign/fourbitsencode.go +++ b/pkg/obialign/fourbitsencode.go @@ -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, diff --git a/pkg/obialign/pairedendalign.go b/pkg/obialign/pairedendalign.go index 4ec22b1..fa543ff 100644 --- a/pkg/obialign/pairedendalign.go +++ b/pkg/obialign/pairedendalign.go @@ -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 { diff --git a/pkg/obiapat/pattern.go b/pkg/obiapat/pattern.go index 528be0f..f915c6c 100644 --- a/pkg/obiapat/pattern.go +++ b/pkg/obiapat/pattern.go @@ -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) diff --git a/pkg/obiapat/pcr.go b/pkg/obiapat/pcr.go index 3bc299e..5f4467e 100644 --- a/pkg/obiapat/pcr.go +++ b/pkg/obiapat/pcr.go @@ -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 { diff --git a/pkg/obiformats/ecopcr_read.go b/pkg/obiformats/ecopcr_read.go index 3557618..10017e6 100644 --- a/pkg/obiformats/ecopcr_read.go +++ b/pkg/obiformats/ecopcr_read.go @@ -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 { diff --git a/pkg/obiformats/embl_read.go b/pkg/obiformats/embl_read.go index aca08f7..3cff6cb 100644 --- a/pkg/obiformats/embl_read.go +++ b/pkg/obiformats/embl_read.go @@ -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 diff --git a/pkg/obiformats/fastseq_header.go b/pkg/obiformats/fastseq_header.go index 9c6fd73..0f9df71 100644 --- a/pkg/obiformats/fastseq_header.go +++ b/pkg/obiformats/fastseq_header.go @@ -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) { diff --git a/pkg/obiformats/fastseq_interface.go b/pkg/obiformats/fastseq_interface.go index b596dce..3a2f70b 100644 --- a/pkg/obiformats/fastseq_interface.go +++ b/pkg/obiformats/fastseq_interface.go @@ -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 diff --git a/pkg/obiformats/fastseq_json_header.go b/pkg/obiformats/fastseq_json_header.go index 4baf46a..5daba14 100644 --- a/pkg/obiformats/fastseq_json_header.go +++ b/pkg/obiformats/fastseq_json_header.go @@ -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" ) diff --git a/pkg/obiformats/fastseq_obi_header.go b/pkg/obiformats/fastseq_obi_header.go index b0c3bc4..950c896 100644 --- a/pkg/obiformats/fastseq_obi_header.go +++ b/pkg/obiformats/fastseq_obi_header.go @@ -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" ) diff --git a/pkg/obiformats/fastseq_read.go b/pkg/obiformats/fastseq_read.go index 36f4e28..89b3231 100644 --- a/pkg/obiformats/fastseq_read.go +++ b/pkg/obiformats/fastseq_read.go @@ -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, diff --git a/pkg/obiformats/fastseq_write_fasta.go b/pkg/obiformats/fastseq_write_fasta.go index b403f7c..2563af2 100644 --- a/pkg/obiformats/fastseq_write_fasta.go +++ b/pkg/obiformats/fastseq_write_fasta.go @@ -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 { diff --git a/pkg/obiformats/fastseq_write_fastq.go b/pkg/obiformats/fastseq_write_fastq.go index 1414e8f..db76eb4 100644 --- a/pkg/obiformats/fastseq_write_fastq.go +++ b/pkg/obiformats/fastseq_write_fastq.go @@ -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 { diff --git a/pkg/obiformats/ncbitaxdump/read.go b/pkg/obiformats/ncbitaxdump/read.go index 40cccdc..75a873b 100644 --- a/pkg/obiformats/ncbitaxdump/read.go +++ b/pkg/obiformats/ncbitaxdump/read.go @@ -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) { diff --git a/pkg/obiformats/options.go b/pkg/obiformats/options.go index 76e578b..089d902 100644 --- a/pkg/obiformats/options.go +++ b/pkg/obiformats/options.go @@ -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 diff --git a/pkg/obiformats/universal_read.go b/pkg/obiformats/universal_read.go index ea888ed..c4bdaa2 100644 --- a/pkg/obiformats/universal_read.go +++ b/pkg/obiformats/universal_read.go @@ -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 { diff --git a/pkg/obiformats/universal_write.go b/pkg/obiformats/universal_write.go index 4c9400e..dd2400b 100644 --- a/pkg/obiformats/universal_write.go +++ b/pkg/obiformats/universal_write.go @@ -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, diff --git a/pkg/obikmer/encodefourmer.go b/pkg/obikmer/encodefourmer.go index 29267e9..14e4cd2 100644 --- a/pkg/obikmer/encodefourmer.go +++ b/pkg/obikmer/encodefourmer.go @@ -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, diff --git a/pkg/obiseq/biosequence.go b/pkg/obiseq/biosequence.go index 3e6d1c4..39cd4fc 100644 --- a/pkg/obiseq/biosequence.go +++ b/pkg/obiseq/biosequence.go @@ -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 diff --git a/pkg/obiseq/join.go b/pkg/obiseq/join.go index ba83f7c..b022397 100644 --- a/pkg/obiseq/join.go +++ b/pkg/obiseq/join.go @@ -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) { diff --git a/pkg/obiseq/subseq.go b/pkg/obiseq/subseq.go index 423e1c9..2255920 100644 --- a/pkg/obiseq/subseq.go +++ b/pkg/obiseq/subseq.go @@ -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, diff --git a/pkg/obitools/obiconvert/sequence_reader.go b/pkg/obitools/obiconvert/sequence_reader.go index 631132a..e6b9cb3 100644 --- a/pkg/obitools/obiconvert/sequence_reader.go +++ b/pkg/obitools/obiconvert/sequence_reader.go @@ -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) { diff --git a/pkg/obitools/obiconvert/sequence_writer.go b/pkg/obitools/obiconvert/sequence_writer.go index bf12520..610a0a4 100644 --- a/pkg/obitools/obiconvert/sequence_writer.go +++ b/pkg/obitools/obiconvert/sequence_writer.go @@ -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 { diff --git a/pkg/obitools/obifind/iterator.go b/pkg/obitools/obifind/iterator.go index c35be5b..cf437cd 100644 --- a/pkg/obitools/obifind/iterator.go +++ b/pkg/obitools/obifind/iterator.go @@ -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 { diff --git a/pkg/obitools/obifind/options.go b/pkg/obitools/obifind/options.go index 49a0d9e..9375d42 100644 --- a/pkg/obitools/obifind/options.go +++ b/pkg/obitools/obifind/options.go @@ -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" ) diff --git a/pkg/obitools/obipairing/options.go b/pkg/obitools/obipairing/options.go index 332634a..687e3ab 100644 --- a/pkg/obitools/obipairing/options.go +++ b/pkg/obitools/obipairing/options.go @@ -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" ) diff --git a/pkg/obitools/obipairing/pairing.go b/pkg/obitools/obipairing/pairing.go index f5c4a4e..c910fb8 100644 --- a/pkg/obitools/obipairing/pairing.go +++ b/pkg/obitools/obipairing/pairing.go @@ -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" ) diff --git a/pkg/obitools/obipcr/options.go b/pkg/obitools/obipcr/options.go index 071d767..fe41711 100644 --- a/pkg/obitools/obipcr/options.go +++ b/pkg/obitools/obipcr/options.go @@ -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" ) diff --git a/pkg/obitools/obipcr/pcr.go b/pkg/obitools/obipcr/pcr.go index 9ae868f..48a40b2 100644 --- a/pkg/obitools/obipcr/pcr.go +++ b/pkg/obitools/obipcr/pcr.go @@ -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) { diff --git a/test/main.go b/test/main.go deleted file mode 100644 index 5d895a8..0000000 --- a/test/main.go +++ /dev/null @@ -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())) -} diff --git a/test/test_test.go b/test/test_test.go deleted file mode 100644 index 4008ad7..0000000 --- a/test/test_test.go +++ /dev/null @@ -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) - -}