mirror of
https://github.com/metabarcoding/obitools4.git
synced 2025-06-29 16:20:46 +00:00
first preliminary version of obiscript.
Former-commit-id: 0d2c0fc5e33e0873ba5c04aca4cf7dd69aa83c90
This commit is contained in:
57
cmd/obitools/obiscript/main.go
Normal file
57
cmd/obitools/obiscript/main.go
Normal file
@ -0,0 +1,57 @@
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package main
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import (
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"fmt"
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"os"
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log "github.com/sirupsen/logrus"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiscript"
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)
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func main() {
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defer obiseq.LogBioSeqStatus()
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// go tool pprof -http=":8000" ./obipairing ./cpu.pprof
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// f, err := os.Create("cpu.pprof")
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// if err != nil {
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// log.Fatal(err)
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// }
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// pprof.StartCPUProfile(f)
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// defer pprof.StopCPUProfile()
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// go tool trace cpu.trace
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// ftrace, err := os.Create("cpu.trace")
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// if err != nil {
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// log.Fatal(err)
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// }
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// trace.Start(ftrace)
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// defer trace.Stop()
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optionParser := obioptions.GenerateOptionParser(obiscript.OptionSet)
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_, args := optionParser(os.Args)
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if obiscript.CLIAskScriptTemplate() {
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fmt.Print(obiscript.CLIScriptTemplate())
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os.Exit(0)
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}
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sequences, err := obiconvert.CLIReadBioSequences(args...)
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if err != nil {
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log.Errorf("Cannot open file (%v)", err)
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os.Exit(1)
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}
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annotator := obiscript.CLIScriptPipeline()
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obiconvert.CLIWriteBioSequences(sequences.Pipe(annotator), true)
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obiiter.WaitForLastPipe()
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}
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18
go.mod
18
go.mod
@ -23,10 +23,22 @@ require (
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)
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require (
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github.com/alecthomas/chroma v0.10.0 // indirect
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github.com/alexeyco/binder v0.0.0-20180729220023-2a21303f588a // indirect
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github.com/chzyer/readline v1.5.0 // indirect
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github.com/davecgh/go-spew v1.1.1 // indirect
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github.com/kr/pretty v0.2.1 // indirect
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github.com/kr/text v0.1.0 // indirect
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github.com/dlclark/regexp2 v1.11.0 // indirect
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github.com/dop251/goja v0.0.0-20240220182346-e401ed450204 // indirect
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github.com/fatih/color v1.16.0 // indirect
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github.com/go-sourcemap/sourcemap v2.1.3+incompatible // indirect
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github.com/google/pprof v0.0.0-20230207041349-798e818bf904 // indirect
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github.com/kr/pretty v0.3.0 // indirect
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github.com/kr/text v0.2.0 // indirect
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github.com/mattn/go-colorable v0.1.13 // indirect
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github.com/mattn/go-isatty v0.0.20 // indirect
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github.com/pmezard/go-difflib v1.0.0 // indirect
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github.com/yuin/gopher-lua v1.1.1 // indirect
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golang.org/x/text v0.13.0 // indirect
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)
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require (
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@ -39,7 +51,7 @@ require (
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github.com/shopspring/decimal v1.3.1 // indirect
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github.com/ulikunitz/xz v0.5.11
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golang.org/x/net v0.17.0 // indirect
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golang.org/x/sys v0.13.0 // indirect
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golang.org/x/sys v0.17.0 // indirect
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golang.org/x/term v0.13.0 // indirect
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gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c
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)
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72
go.sum
72
go.sum
@ -4,22 +4,48 @@ github.com/PaesslerAG/gval v1.2.2 h1:Y7iBzhgE09IGTt5QgGQ2IdaYYYOU134YGHBThD+wm9E
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github.com/PaesslerAG/gval v1.2.2/go.mod h1:XRFLwvmkTEdYziLdaCeCa5ImcGVrfQbeNUbVR+C6xac=
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github.com/PaesslerAG/jsonpath v0.1.0 h1:gADYeifvlqK3R3i2cR5B4DGgxLXIPb3TRTH1mGi0jPI=
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github.com/PaesslerAG/jsonpath v0.1.0/go.mod h1:4BzmtoM/PI8fPO4aQGIusjGxGir2BzcV0grWtFzq1Y8=
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github.com/alecthomas/chroma v0.10.0 h1:7XDcGkCQopCNKjZHfYrNLraA+M7e0fMiJ/Mfikbfjek=
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github.com/alecthomas/chroma v0.10.0/go.mod h1:jtJATyUxlIORhUOFNA9NZDWGAQ8wpxQQqNSB4rjA/1s=
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github.com/alexeyco/binder v0.0.0-20180729220023-2a21303f588a h1:eVFBuipE7TEjIyfrbnQUTG3dBYEtqrRKXSInpyLv41Y=
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github.com/alexeyco/binder v0.0.0-20180729220023-2a21303f588a/go.mod h1:uxLp5y9OziDVlIADUk/fpPnEM479nk3gNNZEotIoKoA=
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github.com/barkimedes/go-deepcopy v0.0.0-20220514131651-17c30cfc62df h1:GSoSVRLoBaFpOOds6QyY1L8AX7uoY+Ln3BHc22W40X0=
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github.com/barkimedes/go-deepcopy v0.0.0-20220514131651-17c30cfc62df/go.mod h1:hiVxq5OP2bUGBRNS3Z/bt/reCLFNbdcST6gISi1fiOM=
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github.com/chen3feng/stl4go v0.1.1 h1:0L1+mDw7pomftKDruM23f1mA7miavOj6C6MZeadzN2Q=
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github.com/chen3feng/stl4go v0.1.1/go.mod h1:5ml3psLgETJjRJnMbPE+JiHLrCpt+Ajc2weeTECXzWU=
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github.com/chzyer/logex v1.2.0/go.mod h1:9+9sk7u7pGNWYMkh0hdiL++6OeibzJccyQU4p4MedaY=
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github.com/chzyer/readline v1.5.0 h1:lSwwFrbNviGePhkewF1az4oLmcwqCZijQ2/Wi3BGHAI=
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github.com/chzyer/readline v1.5.0/go.mod h1:x22KAscuvRqlLoK9CsoYsmxoXZMMFVyOl86cAH8qUic=
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github.com/chzyer/test v0.0.0-20210722231415-061457976a23/go.mod h1:Q3SI9o4m/ZMnBNeIyt5eFwwo7qiLfzFZmjNmxjkiQlU=
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github.com/creack/pty v1.1.9/go.mod h1:oKZEueFk5CKHvIhNR5MUki03XCEU+Q6VDXinZuGJ33E=
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github.com/daichi-m/go18ds v1.12.1 h1:Pjc3IApmN4qtDiovGP9MvMpIzgZle3SHUcNaA5j46bg=
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github.com/daichi-m/go18ds v1.12.1/go.mod h1:wc2dURUr8aMxxC4Mn5ObJGVM7uIKU8JagY4nhtonXq8=
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github.com/davecgh/go-spew v1.1.0/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
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github.com/davecgh/go-spew v1.1.1 h1:vj9j/u1bqnvCEfJOwUhtlOARqs3+rkHYY13jYWTU97c=
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github.com/davecgh/go-spew v1.1.1/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
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github.com/dlclark/regexp2 v1.4.0/go.mod h1:2pZnwuY/m+8K6iRw6wQdMtk+rH5tNGR1i55kozfMjCc=
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github.com/dlclark/regexp2 v1.4.1-0.20201116162257-a2a8dda75c91/go.mod h1:2pZnwuY/m+8K6iRw6wQdMtk+rH5tNGR1i55kozfMjCc=
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github.com/dlclark/regexp2 v1.7.0/go.mod h1:DHkYz0B9wPfa6wondMfaivmHpzrQ3v9q8cnmRbL6yW8=
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github.com/dlclark/regexp2 v1.11.0 h1:G/nrcoOa7ZXlpoa/91N3X7mM3r8eIlMBBJZvsz/mxKI=
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github.com/dlclark/regexp2 v1.11.0/go.mod h1:DHkYz0B9wPfa6wondMfaivmHpzrQ3v9q8cnmRbL6yW8=
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github.com/dop251/goja v0.0.0-20211022113120-dc8c55024d06/go.mod h1:R9ET47fwRVRPZnOGvHxxhuZcbrMCuiqOz3Rlrh4KSnk=
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github.com/dop251/goja v0.0.0-20240220182346-e401ed450204 h1:O7I1iuzEA7SG+dK8ocOBSlYAA9jBUmCYl/Qa7ey7JAM=
|
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github.com/dop251/goja v0.0.0-20240220182346-e401ed450204/go.mod h1:QMWlm50DNe14hD7t24KEqZuUdC9sOTy8W6XbCU1mlw4=
|
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github.com/dop251/goja_nodejs v0.0.0-20210225215109-d91c329300e7/go.mod h1:hn7BA7c8pLvoGndExHudxTDKZ84Pyvv+90pbBjbTz0Y=
|
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github.com/dop251/goja_nodejs v0.0.0-20211022123610-8dd9abb0616d/go.mod h1:DngW8aVqWbuLRMHItjPUyqdj+HWPvnQe8V8y1nDpIbM=
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github.com/dsnet/compress v0.0.1 h1:PlZu0n3Tuv04TzpfPbrnI0HW/YwodEXDS+oPKahKF0Q=
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github.com/dsnet/compress v0.0.1/go.mod h1:Aw8dCMJ7RioblQeTqt88akK31OvO8Dhf5JflhBbQEHo=
|
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github.com/dsnet/golib v0.0.0-20171103203638-1ea166775780/go.mod h1:Lj+Z9rebOhdfkVLjJ8T6VcRQv3SXugXy999NBtR9aFY=
|
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github.com/fatih/color v1.16.0 h1:zmkK9Ngbjj+K0yRhTVONQh1p/HknKYSlNT+vZCzyokM=
|
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github.com/fatih/color v1.16.0/go.mod h1:fL2Sau1YI5c0pdGEVCbKQbLXB6edEj1ZgiY4NijnWvE=
|
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github.com/gabriel-vasile/mimetype v1.4.3 h1:in2uUcidCuFcDKtdcBxlR0rJ1+fsokWf+uqxgUFjbI0=
|
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github.com/gabriel-vasile/mimetype v1.4.3/go.mod h1:d8uq/6HKRL6CGdk+aubisF/M5GcPfT7nKyLpA0lbSSk=
|
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github.com/go-sourcemap/sourcemap v2.1.3+incompatible h1:W1iEw64niKVGogNgBN3ePyLFfuisuzeidWPMPWmECqU=
|
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github.com/go-sourcemap/sourcemap v2.1.3+incompatible/go.mod h1:F8jJfvm2KbVjc5NqelyYJmf/v5J0dwNLS2mL4sNA1Jg=
|
||||
github.com/goccy/go-json v0.10.2 h1:CrxCmQqYDkv1z7lO7Wbh2HN93uovUHgrECaO5ZrCXAU=
|
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github.com/goccy/go-json v0.10.2/go.mod h1:6MelG93GURQebXPDq3khkgXZkazVtN9CRI+MGFi0w8I=
|
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github.com/google/pprof v0.0.0-20230207041349-798e818bf904 h1:4/hN5RUoecvl+RmJRE2YxKWtnnQls6rQjjW5oV7qg2U=
|
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github.com/google/pprof v0.0.0-20230207041349-798e818bf904/go.mod h1:uglQLonpP8qtYCYyzA+8c/9qtqgA3qsXGYqCPKARAFg=
|
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github.com/ianlancetaylor/demangle v0.0.0-20220319035150-800ac71e25c2/go.mod h1:aYm2/VgdVmcIU8iMfdMvDMsRAQjcfZSKFby6HOFvi/w=
|
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github.com/k0kubun/go-ansi v0.0.0-20180517002512-3bf9e2903213/go.mod h1:vNUNkEQ1e29fT/6vq2aBdFsgNPmy8qMdSay1npru+Sw=
|
||||
github.com/klauspost/compress v1.4.1/go.mod h1:RyIbtBH6LamlWaDj8nUwkbUhJ87Yi3uG0guNDohfE1A=
|
||||
github.com/klauspost/compress v1.17.2 h1:RlWWUY/Dr4fL8qk9YG7DTZ7PDgME2V4csBXA8L/ixi4=
|
||||
@ -27,12 +53,22 @@ github.com/klauspost/compress v1.17.2/go.mod h1:ntbaceVETuRiXiv4DpjP66DpAtAGkEQs
|
||||
github.com/klauspost/cpuid v1.2.0/go.mod h1:Pj4uuM528wm8OyEC2QMXAi2YiTZ96dNQPGgoMS4s3ek=
|
||||
github.com/klauspost/pgzip v1.2.6 h1:8RXeL5crjEUFnR2/Sn6GJNWtSQ3Dk8pq4CL3jvdDyjU=
|
||||
github.com/klauspost/pgzip v1.2.6/go.mod h1:Ch1tH69qFZu15pkjo5kYi6mth2Zzwzt50oCQKQE9RUs=
|
||||
github.com/kr/pretty v0.1.0/go.mod h1:dAy3ld7l9f0ibDNOQOHHMYYIIbhfbHSm3C4ZsoJORNo=
|
||||
github.com/kr/pretty v0.2.1 h1:Fmg33tUaq4/8ym9TJN1x7sLJnHVwhP33CNkpYV/7rwI=
|
||||
github.com/kr/pretty v0.2.1/go.mod h1:ipq/a2n7PKx3OHsz4KJII5eveXtPO4qwEXGdVfWzfnI=
|
||||
github.com/kr/pretty v0.3.0 h1:WgNl7dwNpEZ6jJ9k1snq4pZsg7DOEN8hP9Xw0Tsjwk0=
|
||||
github.com/kr/pretty v0.3.0/go.mod h1:640gp4NfQd8pI5XOwp5fnNeVWj67G7CFk/SaSQn7NBk=
|
||||
github.com/kr/pty v1.1.1/go.mod h1:pFQYn66WHrOpPYNljwOMqo10TkYh1fy3cYio2l3bCsQ=
|
||||
github.com/kr/text v0.1.0 h1:45sCR5RtlFHMR4UwH9sdQ5TC8v0qDQCHnXt+kaKSTVE=
|
||||
github.com/kr/text v0.1.0/go.mod h1:4Jbv+DJW3UT/LiOwJeYQe1efqtUx/iVham/4vfdArNI=
|
||||
github.com/kr/text v0.2.0 h1:5Nx0Ya0ZqY2ygV366QzturHI13Jq95ApcVaJBhpS+AY=
|
||||
github.com/kr/text v0.2.0/go.mod h1:eLer722TekiGuMkidMxC/pM04lWEeraHUUmBw8l2grE=
|
||||
github.com/mattn/go-colorable v0.1.13 h1:fFA4WZxdEF4tXPZVKMLwD8oUnCTTo08duU7wxecdEvA=
|
||||
github.com/mattn/go-colorable v0.1.13/go.mod h1:7S9/ev0klgBDR4GtXTXX8a3vIGJpMovkB8vQcUbaXHg=
|
||||
github.com/mattn/go-isatty v0.0.16/go.mod h1:kYGgaQfpe5nmfYZH+SKPsOc2e4SrIfOl2e/yFXSvRLM=
|
||||
github.com/mattn/go-isatty v0.0.17/go.mod h1:kYGgaQfpe5nmfYZH+SKPsOc2e4SrIfOl2e/yFXSvRLM=
|
||||
github.com/mattn/go-isatty v0.0.20 h1:xfD0iDuEKnDkl03q4limB+vH+GxLEtL/jb4xVJSWWEY=
|
||||
github.com/mattn/go-isatty v0.0.20/go.mod h1:W+V8PltTTMOvKvAeJH7IuucS94S2C6jfK/D7dTCTo3Y=
|
||||
github.com/mattn/go-runewidth v0.0.14/go.mod h1:Jdepj2loyihRzMpdS35Xk/zdY8IAYHsh153qUoGf23w=
|
||||
github.com/mattn/go-runewidth v0.0.15 h1:UNAjwbU9l54TA3KzvqLGxwWjHmMgBUVhBiTjelZgg3U=
|
||||
github.com/mattn/go-runewidth v0.0.15/go.mod h1:Jdepj2loyihRzMpdS35Xk/zdY8IAYHsh153qUoGf23w=
|
||||
@ -43,6 +79,7 @@ github.com/pmezard/go-difflib v1.0.0/go.mod h1:iKH77koFhYxTK1pcRnkKkqfTogsbg7gZN
|
||||
github.com/rivo/uniseg v0.2.0/go.mod h1:J6wj4VEh+S6ZtnVlnTBMWIodfgj8LQOQFoIToxlJtxc=
|
||||
github.com/rivo/uniseg v0.4.4 h1:8TfxU8dW6PdqD27gjM8MVNuicgxIjxpm4K7x4jp8sis=
|
||||
github.com/rivo/uniseg v0.4.4/go.mod h1:FN3SvrM+Zdj16jyLfmOkMNblXMcoc8DfTHruCPUcx88=
|
||||
github.com/rogpeppe/go-internal v1.6.1/go.mod h1:xXDCJY+GAPziupqXw64V24skbSoqbTEfhy4qGm1nDQc=
|
||||
github.com/rrethy/ahocorasick v1.0.0 h1:YKkCB+E5PXc0xmLfMrWbfNht8vG9Re97IHSWZk/Lk8E=
|
||||
github.com/rrethy/ahocorasick v1.0.0/go.mod h1:nq8oScE7Vy1rOppoQxpQiiDmPHuKCuk9rXrNcxUV3R0=
|
||||
github.com/schollz/progressbar/v3 v3.13.1 h1:o8rySDYiQ59Mwzy2FELeHY5ZARXZTVJC7iHD6PEFUiE=
|
||||
@ -62,23 +99,58 @@ github.com/traefik/yaegi v0.15.1/go.mod h1:AVRxhaI2G+nUsaM1zyktzwXn69G3t/AuTDrCi
|
||||
github.com/ulikunitz/xz v0.5.6/go.mod h1:2bypXElzHzzJZwzH67Y6wb67pO62Rzfn7BSiF4ABRW8=
|
||||
github.com/ulikunitz/xz v0.5.11 h1:kpFauv27b6ynzBNT/Xy+1k+fK4WswhN/6PN5WhFAGw8=
|
||||
github.com/ulikunitz/xz v0.5.11/go.mod h1:nbz6k7qbPmH4IRqmfOplQw/tblSgqTqBwxkY0oWt/14=
|
||||
github.com/yuin/goldmark v1.4.13/go.mod h1:6yULJ656Px+3vBD8DxQVa3kxgyrAnzto9xy5taEt/CY=
|
||||
github.com/yuin/gopher-lua v1.1.1 h1:kYKnWBjvbNP4XLT3+bPEwAXJx262OhaHDWDVOPjL46M=
|
||||
github.com/yuin/gopher-lua v1.1.1/go.mod h1:GBR0iDaNXjAgGg9zfCvksxSRnQx76gclCIb7kdAd1Pw=
|
||||
golang.org/x/crypto v0.0.0-20190308221718-c2843e01d9a2/go.mod h1:djNgcEr1/C05ACkg1iLfiJU5Ep61QUkGW8qpdssI0+w=
|
||||
golang.org/x/crypto v0.0.0-20210921155107-089bfa567519/go.mod h1:GvvjBRRGRdwPK5ydBHafDWAxML/pGHZbMvKqRZ5+Abc=
|
||||
golang.org/x/exp v0.0.0-20231006140011-7918f672742d h1:jtJma62tbqLibJ5sFQz8bKtEM8rJBtfilJ2qTU199MI=
|
||||
golang.org/x/exp v0.0.0-20231006140011-7918f672742d/go.mod h1:ldy0pHrwJyGW56pPQzzkH36rKxoZW1tw7ZJpeKx+hdo=
|
||||
golang.org/x/mod v0.6.0-dev.0.20220419223038-86c51ed26bb4/go.mod h1:jJ57K6gSWd91VN4djpZkiMVwK6gcyfeH4XE8wZrZaV4=
|
||||
golang.org/x/net v0.0.0-20190620200207-3b0461eec859/go.mod h1:z5CRVTTTmAJ677TzLLGU+0bjPO0LkuOLi4/5GtJWs/s=
|
||||
golang.org/x/net v0.0.0-20210226172049-e18ecbb05110/go.mod h1:m0MpNAwzfU5UDzcl9v0D8zg8gWTRqZa9RBIspLL5mdg=
|
||||
golang.org/x/net v0.0.0-20220722155237-a158d28d115b/go.mod h1:XRhObCWvk6IyKnWLug+ECip1KBveYUHfp+8e9klMJ9c=
|
||||
golang.org/x/net v0.17.0 h1:pVaXccu2ozPjCXewfr1S7xza/zcXTity9cCdXQYSjIM=
|
||||
golang.org/x/net v0.17.0/go.mod h1:NxSsAGuq816PNPmqtQdLE42eU2Fs7NoRIZrHJAlaCOE=
|
||||
golang.org/x/sync v0.0.0-20190423024810-112230192c58/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM=
|
||||
golang.org/x/sync v0.0.0-20220722155255-886fb9371eb4/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM=
|
||||
golang.org/x/sys v0.0.0-20190215142949-d0b11bdaac8a/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY=
|
||||
golang.org/x/sys v0.0.0-20201119102817-f84b799fce68/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
|
||||
golang.org/x/sys v0.0.0-20210615035016-665e8c7367d1/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
|
||||
golang.org/x/sys v0.0.0-20220310020820-b874c991c1a5/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
|
||||
golang.org/x/sys v0.0.0-20220520151302-bc2c85ada10a/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
|
||||
golang.org/x/sys v0.0.0-20220715151400-c0bba94af5f8/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
|
||||
golang.org/x/sys v0.0.0-20220722155257-8c9f86f7a55f/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
|
||||
golang.org/x/sys v0.0.0-20220811171246-fbc7d0a398ab/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
|
||||
golang.org/x/sys v0.6.0/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
|
||||
golang.org/x/sys v0.13.0 h1:Af8nKPmuFypiUBjVoU9V20FiaFXOcuZI21p0ycVYYGE=
|
||||
golang.org/x/sys v0.13.0/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
|
||||
golang.org/x/sys v0.17.0 h1:25cE3gD+tdBA7lp7QfhuV+rJiE9YXTcS3VG1SqssI/Y=
|
||||
golang.org/x/sys v0.17.0/go.mod h1:/VUhepiaJMQUp4+oa/7Zr1D23ma6VTLIYjOOTFZPUcA=
|
||||
golang.org/x/term v0.0.0-20201126162022-7de9c90e9dd1/go.mod h1:bj7SfCRtBDWHUb9snDiAeCFNEtKQo2Wmx5Cou7ajbmo=
|
||||
golang.org/x/term v0.0.0-20210927222741-03fcf44c2211/go.mod h1:jbD1KX2456YbFQfuXm/mYQcufACuNUgVhRMnK/tPxf8=
|
||||
golang.org/x/term v0.6.0/go.mod h1:m6U89DPEgQRMq3DNkDClhWw02AUbt2daBVO4cn4Hv9U=
|
||||
golang.org/x/term v0.13.0 h1:bb+I9cTfFazGW51MZqBVmZy7+JEJMouUHTUSKVQLBek=
|
||||
golang.org/x/term v0.13.0/go.mod h1:LTmsnFJwVN6bCy1rVCoS+qHT1HhALEFxKncY3WNNh4U=
|
||||
golang.org/x/text v0.3.0/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ=
|
||||
golang.org/x/text v0.3.3/go.mod h1:5Zoc/QRtKVWzQhOtBMvqHzDpF6irO9z98xDceosuGiQ=
|
||||
golang.org/x/text v0.3.6/go.mod h1:5Zoc/QRtKVWzQhOtBMvqHzDpF6irO9z98xDceosuGiQ=
|
||||
golang.org/x/text v0.3.7/go.mod h1:u+2+/6zg+i71rQMx5EYifcz6MCKuco9NR6JIITiCfzQ=
|
||||
golang.org/x/text v0.3.8/go.mod h1:E6s5w1FMmriuDzIBO73fBruAKo1PCIq6d2Q6DHfQ8WQ=
|
||||
golang.org/x/text v0.13.0 h1:ablQoSUd0tRdKxZewP80B+BaqeKJuVhuRxj/dkrun3k=
|
||||
golang.org/x/text v0.13.0/go.mod h1:TvPlkZtksWOMsz7fbANvkp4WM8x/WCo/om8BMLbz+aE=
|
||||
golang.org/x/tools v0.0.0-20180917221912-90fa682c2a6e/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ=
|
||||
golang.org/x/tools v0.0.0-20191119224855-298f0cb1881e/go.mod h1:b+2E5dAYhXwXZwtnZ6UAqBI28+e2cm9otk0dWdXHAEo=
|
||||
golang.org/x/tools v0.1.12/go.mod h1:hNGJHUnrk76NpqgfD5Aqm5Crs+Hm0VOH/i9J2+nxYbc=
|
||||
golang.org/x/xerrors v0.0.0-20190717185122-a985d3407aa7/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0=
|
||||
gonum.org/v1/gonum v0.14.0 h1:2NiG67LD1tEH0D7kM+ps2V+fXmsAnpUeec7n8tcr4S0=
|
||||
gonum.org/v1/gonum v0.14.0/go.mod h1:AoWeoz0becf9QMWtE8iWXNXc27fK4fNeHNf/oMejGfU=
|
||||
gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
|
||||
gopkg.in/check.v1 v1.0.0-20180628173108-788fd7840127/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
|
||||
gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c h1:Hei/4ADfdWqJk1ZMxUNpqntNwaWcugrBjAiHlqqRiVk=
|
||||
gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c/go.mod h1:JHkPIbrfpd72SG/EVd6muEfDQjcINNoR0C8j2r3qZ4Q=
|
||||
gopkg.in/errgo.v2 v2.1.0/go.mod h1:hNsd1EY+bozCKY1Ytp96fpM3vjJbqLJn88ws8XvfDNI=
|
||||
gopkg.in/yaml.v2 v2.4.0/go.mod h1:RDklbk79AGWmwhnvt/jBztapEOGDOx6ZbXqjP6csGnQ=
|
||||
gopkg.in/yaml.v3 v3.0.0-20200313102051-9f266ea9e77c/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM=
|
||||
gopkg.in/yaml.v3 v3.0.1 h1:fxVm/GzAzEWqLHuvctI91KS9hhNmmWOoWu0XTYJS7CA=
|
||||
gopkg.in/yaml.v3 v3.0.1/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM=
|
||||
|
||||
@ -2,6 +2,9 @@ git.sr.ht/~sbinet/gg v0.3.1 h1:LNhjNn8DerC8f9DHLz6lS0YYul/b602DUxDgGkd/Aik=
|
||||
git.sr.ht/~sbinet/gg v0.3.1/go.mod h1:KGYtlADtqsqANL9ueOFkWymvzUvLMQllU5Ixo+8v3pc=
|
||||
github.com/ajstarks/svgo v0.0.0-20211024235047-1546f124cd8b h1:slYM766cy2nI3BwyRiyQj/Ud48djTMtMebDqepE95rw=
|
||||
github.com/ajstarks/svgo v0.0.0-20211024235047-1546f124cd8b/go.mod h1:1KcenG0jGWcpt8ov532z81sp/kMMUG485J2InIOyADM=
|
||||
github.com/chzyer/logex v1.1.10/go.mod h1:+Ywpsq7O8HXn0nuIou7OrIPyXbp3wmkHB+jjWRnGsAI=
|
||||
github.com/chzyer/readline v0.0.0-20180603132655-2972be24d48e/go.mod h1:nSuG5e5PlCu98SY8svDHJxuZscDgtXS6KTTbou5AhLI=
|
||||
github.com/chzyer/test v0.0.0-20180213035817-a1ea475d72b1/go.mod h1:Q3SI9o4m/ZMnBNeIyt5eFwwo7qiLfzFZmjNmxjkiQlU=
|
||||
github.com/dsnet/golib v0.0.0-20171103203638-1ea166775780 h1:tFh1tRc4CA31yP6qDcu+Trax5wW5GuMxvkIba07qVLY=
|
||||
github.com/go-fonts/liberation v0.3.0 h1:3BI2iaE7R/s6uUUtzNCjo3QijJu3aS4wmrMgfSpYQ+8=
|
||||
github.com/go-fonts/liberation v0.3.0/go.mod h1:jdJ+cqF+F4SUL2V+qxBth8fvBpBDS7yloUL5Fi8GTGY=
|
||||
@ -19,6 +22,7 @@ github.com/k0kubun/go-ansi v0.0.0-20180517002512-3bf9e2903213 h1:qGQQKEcAR99REcM
|
||||
github.com/klauspost/cpuid v1.2.0 h1:NMpwD2G9JSFOE1/TJjGSo5zG7Yb2bTe7eq1jH+irmeE=
|
||||
github.com/kr/pty v1.1.1 h1:VkoXIwSboBpnk99O/KFauAEILuNHv5DVFKZMBN/gUgw=
|
||||
github.com/mattn/go-isatty v0.0.17 h1:BTarxUcIeDqL27Mc+vyvdWYSL28zpIhv3RoTdsLMPng=
|
||||
github.com/rogpeppe/go-internal v1.6.1 h1:/FiVV8dS/e+YqF2JvO3yXRFbBLTIuSDkuC7aBOAvL+k=
|
||||
github.com/stretchr/objx v0.1.0 h1:4G4v2dO3VZwixGIRoQ5Lfboy6nUhCyYzaqnIAPPhYs4=
|
||||
golang.org/x/crypto v0.14.0 h1:wBqGXzWJW6m1XrIKlAH0Hs1JJ7+9KBwnIO8v66Q9cHc=
|
||||
golang.org/x/crypto v0.14.0/go.mod h1:MVFd36DqK4CsrnJYDkBA3VC4m2GkXAM0PvzMCn4JQf4=
|
||||
@ -26,7 +30,6 @@ golang.org/x/image v0.6.0 h1:bR8b5okrPI3g/gyZakLZHeWxAR8Dn5CyxXv1hLH5g/4=
|
||||
golang.org/x/image v0.6.0/go.mod h1:MXLdDR43H7cDJq5GEGXEVeeNhPgi+YYEQ2pC1byI1x0=
|
||||
golang.org/x/mod v0.13.0 h1:I/DsJXRlw/8l/0c24sM9yb0T4z9liZTduXvdAWYiysY=
|
||||
golang.org/x/mod v0.13.0/go.mod h1:hTbmBsO62+eylJbnUtE2MGJUyE7QWk4xUqPFrRgJ+7c=
|
||||
golang.org/x/text v0.13.0 h1:ablQoSUd0tRdKxZewP80B+BaqeKJuVhuRxj/dkrun3k=
|
||||
golang.org/x/text v0.13.0/go.mod h1:TvPlkZtksWOMsz7fbANvkp4WM8x/WCo/om8BMLbz+aE=
|
||||
golang.org/x/tools v0.14.0 h1:jvNa2pY0M4r62jkRQ6RwEZZyPcymeL9XZMLBbV7U2nc=
|
||||
golang.org/x/tools v0.14.0/go.mod h1:uYBEerGOWcJyEORxN+Ek8+TT266gXkNlHdJBwexUsBg=
|
||||
|
||||
140
pkg/obilua/lua.go
Normal file
140
pkg/obilua/lua.go
Normal file
@ -0,0 +1,140 @@
|
||||
package obilua
|
||||
|
||||
import (
|
||||
"bytes"
|
||||
"os"
|
||||
|
||||
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
|
||||
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
|
||||
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
|
||||
log "github.com/sirupsen/logrus"
|
||||
lua "github.com/yuin/gopher-lua"
|
||||
"github.com/yuin/gopher-lua/parse"
|
||||
)
|
||||
|
||||
func NewInterpreter() *lua.LState {
|
||||
lua := lua.NewState()
|
||||
|
||||
RegisterObilib(lua)
|
||||
|
||||
return lua
|
||||
}
|
||||
|
||||
func Compile(program []byte, name string) (*lua.FunctionProto, error) {
|
||||
|
||||
reader := bytes.NewReader(program)
|
||||
chunk, err := parse.Parse(reader, name)
|
||||
if err != nil {
|
||||
return nil, err
|
||||
}
|
||||
|
||||
proto, err := lua.Compile(chunk, name)
|
||||
if err != nil {
|
||||
return nil, err
|
||||
}
|
||||
return proto, nil
|
||||
}
|
||||
|
||||
func CompileScript(filePath string) (*lua.FunctionProto, error) {
|
||||
program, err := os.ReadFile(filePath)
|
||||
|
||||
if err != nil {
|
||||
return nil, err
|
||||
}
|
||||
|
||||
return Compile(program, filePath)
|
||||
}
|
||||
|
||||
func LuaWorker(proto *lua.FunctionProto) obiseq.SeqWorker {
|
||||
interpreter := NewInterpreter()
|
||||
lfunc := interpreter.NewFunctionFromProto(proto)
|
||||
|
||||
f := func(sequence *obiseq.BioSequence) (obiseq.BioSequenceSlice, error) {
|
||||
interpreter.SetGlobal("sequence", obiseq2Lua(interpreter, sequence))
|
||||
interpreter.Push(lfunc)
|
||||
err := interpreter.PCall(0, lua.MultRet, nil)
|
||||
|
||||
return obiseq.BioSequenceSlice{sequence}, err
|
||||
}
|
||||
|
||||
return f
|
||||
}
|
||||
|
||||
func LuaProcessor(iterator obiiter.IBioSequence, name, program string, breakOnError bool, nworkers int) obiiter.IBioSequence {
|
||||
newIter := obiiter.MakeIBioSequence()
|
||||
|
||||
if nworkers <= 0 {
|
||||
nworkers = obioptions.CLIParallelWorkers()
|
||||
}
|
||||
|
||||
newIter.Add(nworkers)
|
||||
|
||||
go func() {
|
||||
newIter.WaitAndClose()
|
||||
}()
|
||||
|
||||
bp := []byte(program)
|
||||
proto, err := Compile(bp, name)
|
||||
|
||||
if err != nil {
|
||||
log.Fatalf("Cannot compile script %s : %v", name, err)
|
||||
}
|
||||
|
||||
ff := func(iterator obiiter.IBioSequence) {
|
||||
w := LuaWorker(proto)
|
||||
sw := obiseq.SeqToSliceWorker(w, false)
|
||||
|
||||
// iterator = iterator.SortBatches()
|
||||
|
||||
for iterator.Next() {
|
||||
seqs := iterator.Get()
|
||||
slice := seqs.Slice()
|
||||
ns, err := sw(slice)
|
||||
|
||||
if err != nil {
|
||||
if breakOnError {
|
||||
log.Fatalf("Error during Lua sequence processing : %v", err)
|
||||
} else {
|
||||
log.Warnf("Error during Lua sequence processing : %v", err)
|
||||
}
|
||||
}
|
||||
|
||||
newIter.Push(obiiter.MakeBioSequenceBatch(seqs.Order(), ns))
|
||||
seqs.Recycle(false)
|
||||
}
|
||||
|
||||
newIter.Done()
|
||||
}
|
||||
|
||||
for i := 1; i < nworkers; i++ {
|
||||
go ff(iterator.Split())
|
||||
}
|
||||
|
||||
go ff(iterator)
|
||||
|
||||
if iterator.IsPaired() {
|
||||
newIter.MarkAsPaired()
|
||||
}
|
||||
|
||||
return newIter
|
||||
|
||||
}
|
||||
|
||||
func LuaPipe(name, program string, breakOnError bool, nworkers int) obiiter.Pipeable {
|
||||
|
||||
f := func(input obiiter.IBioSequence) obiiter.IBioSequence {
|
||||
return LuaProcessor(input, name, program, breakOnError, nworkers)
|
||||
}
|
||||
|
||||
return f
|
||||
}
|
||||
|
||||
func LuaScriptPipe(filename string, breakOnError bool, nworkers int) obiiter.Pipeable {
|
||||
program, err := os.ReadFile(filename)
|
||||
|
||||
if err != nil {
|
||||
log.Fatalf("Cannot read script file %s", filename)
|
||||
}
|
||||
|
||||
return LuaPipe(filename, string(program), breakOnError, nworkers)
|
||||
}
|
||||
193
pkg/obilua/lua_push_interface.go
Normal file
193
pkg/obilua/lua_push_interface.go
Normal file
@ -0,0 +1,193 @@
|
||||
package obilua
|
||||
|
||||
import (
|
||||
"log"
|
||||
|
||||
lua "github.com/yuin/gopher-lua"
|
||||
)
|
||||
|
||||
// pushInterfaceToLua converts a Go interface{} value to an equivalent Lua value and pushes it onto the stack.
|
||||
//
|
||||
// L *lua.LState: the Lua state onto which the value will be pushed.
|
||||
// val interface{}: the Go interface value to be converted and pushed. This can be a basic type such as string, bool, int, float64,
|
||||
// or slices and maps of these basic types. Custom complex types will be converted to userdata with a predefined metatable.
|
||||
//
|
||||
// No return values. This function operates directly on the Lua state stack.
|
||||
func pushInterfaceToLua(L *lua.LState, val interface{}) {
|
||||
switch v := val.(type) {
|
||||
case string:
|
||||
L.Push(lua.LString(v))
|
||||
case bool:
|
||||
L.Push(lua.LBool(v))
|
||||
case int:
|
||||
L.Push(lua.LNumber(v))
|
||||
case float64:
|
||||
L.Push(lua.LNumber(v))
|
||||
// Add other cases as needed for different types
|
||||
case map[string]int:
|
||||
pushMapStringIntToLua(L, v)
|
||||
case map[string]string:
|
||||
pushMapStringStringToLua(L, v)
|
||||
case map[string]bool:
|
||||
pushMapStringBoolToLua(L, v)
|
||||
case map[string]float64:
|
||||
pushMapStringFloat64ToLua(L, v)
|
||||
case []string:
|
||||
pushSliceStringToLua(L, v)
|
||||
case []int:
|
||||
pushSliceIntToLua(L, v)
|
||||
case []float64:
|
||||
pushSliceFloat64ToLua(L, v)
|
||||
case []bool:
|
||||
pushSliceBoolToLua(L, v)
|
||||
case nil:
|
||||
L.Push(lua.LNil)
|
||||
default:
|
||||
log.Fatalf("Cannot deal with value Mv", val)
|
||||
}
|
||||
}
|
||||
|
||||
// pushMapStringIntToLua creates a new Lua table and iterates over the Go map to set key-value pairs in the Lua table. It then pushes the Lua table onto the stack.
|
||||
//
|
||||
// L *lua.LState - the Lua state
|
||||
// m map[string]int - the Go map containing string to int key-value pairs
|
||||
func pushMapStringIntToLua(L *lua.LState, m map[string]int) {
|
||||
// Create a new Lua table
|
||||
luaTable := L.NewTable()
|
||||
|
||||
// Iterate over the Go map and set the key-value pairs in the Lua table
|
||||
for key, value := range m {
|
||||
L.SetField(luaTable, key, lua.LNumber(value))
|
||||
}
|
||||
|
||||
// Push the Lua table onto the stack
|
||||
L.Push(luaTable)
|
||||
}
|
||||
|
||||
// pushMapStringStringToLua creates a new Lua table and sets key-value pairs from the Go map, then pushes the Lua table onto the stack.
|
||||
//
|
||||
// L *lua.LState, m map[string]string. No return value.
|
||||
func pushMapStringStringToLua(L *lua.LState, m map[string]string) {
|
||||
// Create a new Lua table
|
||||
luaTable := L.NewTable()
|
||||
|
||||
// Iterate over the Go map and set the key-value pairs in the Lua table
|
||||
for key, value := range m {
|
||||
L.SetField(luaTable, key, lua.LString(value))
|
||||
}
|
||||
|
||||
// Push the Lua table onto the stack
|
||||
L.Push(luaTable)
|
||||
}
|
||||
|
||||
// pushMapStringBoolToLua creates a new Lua table, iterates over the Go map, sets the key-value pairs in the Lua table, and then pushes the Lua table onto the stack.
|
||||
//
|
||||
// Parameters:
|
||||
//
|
||||
// L *lua.LState - the Lua state
|
||||
// m map[string]bool - the Go map
|
||||
//
|
||||
// Return type(s): None
|
||||
func pushMapStringBoolToLua(L *lua.LState, m map[string]bool) {
|
||||
// Create a new Lua table
|
||||
luaTable := L.NewTable()
|
||||
|
||||
// Iterate over the Go map and set the key-value pairs in the Lua table
|
||||
for key, value := range m {
|
||||
L.SetField(luaTable, key, lua.LBool(value))
|
||||
}
|
||||
|
||||
// Push the Lua table onto the stack
|
||||
L.Push(luaTable)
|
||||
}
|
||||
|
||||
// pushMapStringFloat64ToLua pushes a map of string-float64 pairs to a Lua table on the stack.
|
||||
//
|
||||
// L *lua.LState - the Lua state
|
||||
// m map[string]float64 - the map to be pushed to Lua
|
||||
func pushMapStringFloat64ToLua(L *lua.LState, m map[string]float64) {
|
||||
// Create a new Lua table
|
||||
luaTable := L.NewTable()
|
||||
|
||||
// Iterate over the Go map and set the key-value pairs in the Lua table
|
||||
for key, value := range m {
|
||||
// Use lua.LNumber since Lua does not differentiate between float and int
|
||||
L.SetField(luaTable, key, lua.LNumber(value))
|
||||
}
|
||||
|
||||
// Push the Lua table onto the stack
|
||||
L.Push(luaTable)
|
||||
}
|
||||
|
||||
// pushSliceIntToLua creates a new Lua table and sets the elements of a Go slice in the Lua table. Then, it pushes the Lua table onto the stack.
|
||||
//
|
||||
// L *lua.LState, slice []int
|
||||
// None
|
||||
func pushSliceIntToLua(L *lua.LState, slice []int) {
|
||||
// Create a new Lua table
|
||||
luaTable := L.NewTable()
|
||||
|
||||
// Iterate over the Go slice and set the elements in the Lua table
|
||||
for _, value := range slice {
|
||||
// Append the value to the Lua table
|
||||
// Lua is 1-indexed, so we use the length of the table + 1 as the next index
|
||||
luaTable.Append(lua.LNumber(value))
|
||||
}
|
||||
|
||||
// Push the Lua table onto the stack
|
||||
L.Push(luaTable)
|
||||
}
|
||||
|
||||
// pushSliceStringToLua creates a new Lua table and sets the elements in the table from the given Go slice. It then pushes the Lua table onto the stack.
|
||||
//
|
||||
// L *lua.LState - The Lua state
|
||||
// slice []string - The Go slice of strings
|
||||
func pushSliceStringToLua(L *lua.LState, slice []string) {
|
||||
// Create a new Lua table
|
||||
luaTable := L.NewTable()
|
||||
|
||||
// Iterate over the Go slice and set the elements in the Lua table
|
||||
for _, value := range slice {
|
||||
// Append the value to the Lua table
|
||||
luaTable.Append(lua.LString(value))
|
||||
}
|
||||
|
||||
// Push the Lua table onto the stack
|
||||
L.Push(luaTable)
|
||||
}
|
||||
|
||||
// pushSliceBoolToLua creates a new Lua table and pushes the boolean values from the given slice onto the Lua stack.
|
||||
//
|
||||
// L *lua.LState - the Lua state
|
||||
// slice []bool - the Go slice containing boolean values
|
||||
func pushSliceBoolToLua(L *lua.LState, slice []bool) {
|
||||
// Create a new Lua table
|
||||
luaTable := L.NewTable()
|
||||
|
||||
// Iterate over the Go slice and insert each boolean into the Lua table
|
||||
for _, value := range slice {
|
||||
// Lua is 1-indexed, so we use the length of the table + 1 as the next index
|
||||
luaTable.Append(lua.LBool(value))
|
||||
}
|
||||
|
||||
// Push the Lua table onto the stack
|
||||
L.Push(luaTable)
|
||||
}
|
||||
|
||||
// pushSliceFloat64ToLua creates a new Lua table and pushes it onto the stack.
|
||||
//
|
||||
// L *lua.LState - the Lua state
|
||||
// slice []float64 - the Go slice to be inserted into the Lua table
|
||||
func pushSliceFloat64ToLua(L *lua.LState, slice []float64) {
|
||||
// Create a new Lua table
|
||||
luaTable := L.NewTable()
|
||||
|
||||
// Iterate over the Go slice and insert each float64 into the Lua table
|
||||
for _, value := range slice {
|
||||
// Lua is 1-indexed, so we append the value to the Lua table
|
||||
luaTable.Append(lua.LNumber(value))
|
||||
}
|
||||
|
||||
// Push the Lua table onto the stack
|
||||
L.Push(luaTable)
|
||||
}
|
||||
7
pkg/obilua/obilib.go
Normal file
7
pkg/obilua/obilib.go
Normal file
@ -0,0 +1,7 @@
|
||||
package obilua
|
||||
|
||||
import lua "github.com/yuin/gopher-lua"
|
||||
|
||||
func RegisterObilib(luaState *lua.LState) {
|
||||
RegisterObiSeq(luaState)
|
||||
}
|
||||
154
pkg/obilua/obiseq.go
Normal file
154
pkg/obilua/obiseq.go
Normal file
@ -0,0 +1,154 @@
|
||||
package obilua
|
||||
|
||||
import (
|
||||
log "github.com/sirupsen/logrus"
|
||||
|
||||
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
|
||||
lua "github.com/yuin/gopher-lua"
|
||||
)
|
||||
|
||||
func RegisterObiSeq(luaState *lua.LState) {
|
||||
registerBioSequenceType(luaState)
|
||||
}
|
||||
|
||||
const luaBioSequenceTypeName = "BioSequence"
|
||||
|
||||
func registerBioSequenceType(luaState *lua.LState) {
|
||||
bioSequenceType := luaState.NewTypeMetatable(luaBioSequenceTypeName)
|
||||
luaState.SetGlobal(luaBioSequenceTypeName, bioSequenceType)
|
||||
luaState.SetField(bioSequenceType, "new", luaState.NewFunction(newObiSeq))
|
||||
|
||||
luaState.SetField(bioSequenceType, "__index",
|
||||
luaState.SetFuncs(luaState.NewTable(),
|
||||
bioSequenceMethods))
|
||||
}
|
||||
|
||||
func obiseq2Lua(interpreter *lua.LState,
|
||||
sequence *obiseq.BioSequence) lua.LValue {
|
||||
ud := interpreter.NewUserData()
|
||||
ud.Value = sequence
|
||||
interpreter.SetMetatable(ud, interpreter.GetTypeMetatable(luaBioSequenceTypeName))
|
||||
|
||||
return ud
|
||||
}
|
||||
func newObiSeq(luaState *lua.LState) int {
|
||||
seqid := luaState.CheckString(1)
|
||||
seq := []byte(luaState.CheckString(2))
|
||||
|
||||
definition := ""
|
||||
if luaState.GetTop() > 2 {
|
||||
definition = luaState.CheckString(3)
|
||||
}
|
||||
|
||||
sequence := obiseq.NewBioSequence(seqid, seq, definition)
|
||||
|
||||
luaState.Push(obiseq2Lua(luaState, sequence))
|
||||
return 1
|
||||
}
|
||||
|
||||
var bioSequenceMethods = map[string]lua.LGFunction{
|
||||
"id": bioSequenceGetSetId,
|
||||
"sequence": bioSequenceGetSetSequence,
|
||||
"definition": bioSequenceGetSetDefinition,
|
||||
"count": bioSequenceGetSetCount,
|
||||
"taxid": bioSequenceGetSetTaxid,
|
||||
"attribute": bioSequenceGetSetAttribute,
|
||||
}
|
||||
|
||||
// checkBioSequence checks if the first argument in the Lua stack is a *obiseq.BioSequence.
|
||||
//
|
||||
// This function accepts a pointer to the Lua state and attempts to retrieve a userdata
|
||||
// that holds a pointer to a BioSequence. If the conversion is successful, it returns
|
||||
// the *BioSequence. If the conversion fails, it raises a Lua argument error.
|
||||
// Returns a pointer to obiseq.BioSequence or nil if the argument is not of the expected type.
|
||||
func checkBioSequence(L *lua.LState) *obiseq.BioSequence {
|
||||
ud := L.CheckUserData(1)
|
||||
if v, ok := ud.Value.(*obiseq.BioSequence); ok {
|
||||
return v
|
||||
}
|
||||
L.ArgError(1, "obiseq.BioSequence expected")
|
||||
return nil
|
||||
}
|
||||
|
||||
// bioSequenceGetSetId gets the ID of a biosequence or sets a new ID if provided.
|
||||
//
|
||||
// This function expects a *lua.LState pointer as its only parameter.
|
||||
// If a second argument is provided, it sets the new ID for the biosequence.
|
||||
// It returns 0 if a new ID is set, or 1 after pushing the current ID onto the stack.
|
||||
func bioSequenceGetSetId(luaState *lua.LState) int {
|
||||
s := checkBioSequence(luaState)
|
||||
if luaState.GetTop() == 2 {
|
||||
s.SetId(luaState.CheckString(2))
|
||||
return 0
|
||||
}
|
||||
luaState.Push(lua.LString(s.Id()))
|
||||
return 1
|
||||
}
|
||||
|
||||
func bioSequenceGetSetSequence(luaState *lua.LState) int {
|
||||
s := checkBioSequence(luaState)
|
||||
if luaState.GetTop() == 2 {
|
||||
s.SetSequence([]byte(luaState.CheckString(2)))
|
||||
return 0
|
||||
}
|
||||
luaState.Push(lua.LString(s.String()))
|
||||
return 1
|
||||
}
|
||||
|
||||
func bioSequenceGetSetDefinition(luaState *lua.LState) int {
|
||||
s := checkBioSequence(luaState)
|
||||
if luaState.GetTop() == 2 {
|
||||
s.SetDefinition(luaState.CheckString(2))
|
||||
return 0
|
||||
}
|
||||
luaState.Push(lua.LString(s.Definition()))
|
||||
return 1
|
||||
}
|
||||
|
||||
func bioSequenceGetSetCount(luaState *lua.LState) int {
|
||||
s := checkBioSequence(luaState)
|
||||
if luaState.GetTop() == 2 {
|
||||
s.SetCount(luaState.CheckInt(2))
|
||||
return 0
|
||||
}
|
||||
luaState.Push(lua.LNumber(s.Count()))
|
||||
return 1
|
||||
}
|
||||
|
||||
func bioSequenceGetSetTaxid(luaState *lua.LState) int {
|
||||
s := checkBioSequence(luaState)
|
||||
if luaState.GetTop() == 2 {
|
||||
s.SetTaxid(luaState.CheckInt(2))
|
||||
return 0
|
||||
}
|
||||
luaState.Push(lua.LNumber(s.Taxid()))
|
||||
return 1
|
||||
}
|
||||
|
||||
func bioSequenceGetSetAttribute(luaState *lua.LState) int {
|
||||
s := checkBioSequence(luaState)
|
||||
attName := luaState.CheckString(2)
|
||||
|
||||
if luaState.GetTop() == 3 {
|
||||
ud := luaState.CheckAny(3)
|
||||
|
||||
log.Infof("ud : %v [%v]", ud, ud.Type())
|
||||
//
|
||||
// Perhaps the code needs some type checking on ud.Value
|
||||
// It's a first test
|
||||
//
|
||||
|
||||
s.SetAttribute(attName, ud)
|
||||
return 0
|
||||
}
|
||||
|
||||
value, ok := s.GetAttribute(attName)
|
||||
|
||||
if !ok {
|
||||
luaState.Push(lua.LNil)
|
||||
} else {
|
||||
pushInterfaceToLua(luaState, value)
|
||||
}
|
||||
|
||||
return 1
|
||||
}
|
||||
14
pkg/obitools/obiscript/obiscript.go
Normal file
14
pkg/obitools/obiscript/obiscript.go
Normal file
@ -0,0 +1,14 @@
|
||||
package obiscript
|
||||
|
||||
import (
|
||||
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
|
||||
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obilua"
|
||||
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
|
||||
)
|
||||
|
||||
func CLIScriptPipeline() obiiter.Pipeable {
|
||||
|
||||
pipe := obilua.LuaScriptPipe(CLIScriptFilename(), true, obioptions.CLIParallelWorkers())
|
||||
|
||||
return pipe
|
||||
}
|
||||
83
pkg/obitools/obiscript/options.go
Normal file
83
pkg/obitools/obiscript/options.go
Normal file
@ -0,0 +1,83 @@
|
||||
package obiscript
|
||||
|
||||
import (
|
||||
"log"
|
||||
"os"
|
||||
|
||||
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
|
||||
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obigrep"
|
||||
"github.com/DavidGamba/go-getoptions"
|
||||
)
|
||||
|
||||
var _script = ""
|
||||
var _askTemplate = false
|
||||
|
||||
func ScriptOptionSet(options *getoptions.GetOpt) {
|
||||
|
||||
options.StringVar(&_script, "script", _script,
|
||||
options.Description("The script to execute."),
|
||||
options.Alias("S"),
|
||||
options.Description("Name of a map attribute."))
|
||||
|
||||
options.BoolVar(&_askTemplate, "template", _askTemplate,
|
||||
options.Description("Print on the standard output a script template."),
|
||||
)
|
||||
}
|
||||
|
||||
func OptionSet(options *getoptions.GetOpt) {
|
||||
ScriptOptionSet(options)
|
||||
obiconvert.OptionSet(options)
|
||||
obigrep.SequenceSelectionOptionSet(options)
|
||||
}
|
||||
|
||||
func CLIScriptFilename() string {
|
||||
return _script
|
||||
}
|
||||
|
||||
func CLIScript() string {
|
||||
file, err := os.ReadFile(_script) // Reads the script
|
||||
if err != nil {
|
||||
log.Fatalf("cannot read the script file : %s", _script)
|
||||
}
|
||||
return string(file)
|
||||
}
|
||||
|
||||
func CLIAskScriptTemplate() bool {
|
||||
return _askTemplate
|
||||
}
|
||||
|
||||
func CLIScriptTemplate() string {
|
||||
return `
|
||||
import {
|
||||
"sync"
|
||||
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
|
||||
}
|
||||
//
|
||||
// Begin function run before the first sequence being processed
|
||||
//
|
||||
|
||||
func Begin(environment *sync.Map) {
|
||||
|
||||
}
|
||||
|
||||
//
|
||||
// Begin function run after the last sequence being processed
|
||||
//
|
||||
|
||||
func End(environment *sync.Map) {
|
||||
|
||||
}
|
||||
|
||||
//
|
||||
// Worker function run for each sequence validating the selection predicat as specified by
|
||||
// the command line options.
|
||||
//
|
||||
// The function must return the altered sequence.
|
||||
// If the function returns nil, the sequence is discarded from the output
|
||||
func Worker(sequence *obiseq.BioSequence, environment *sync.Map) *obiseq.BioSequence {
|
||||
|
||||
|
||||
return sequence
|
||||
}
|
||||
`
|
||||
}
|
||||
Reference in New Issue
Block a user