From e25c3b7365aa0ef206434e74f298abfb36588428 Mon Sep 17 00:00:00 2001 From: Eric Coissac Date: Tue, 19 Mar 2024 13:50:13 +0100 Subject: [PATCH] Bug in the json parsing Former-commit-id: e652b04b9fa7e11124eb5930c7bec4613c808758 --- Makefile | 8 +++--- Release-notes.md | 13 +++++++++- go.mod | 17 +++---------- go.sum | 66 +----------------------------------------------- go.work | 2 +- go.work.sum | 15 ++++++++++- 6 files changed, 35 insertions(+), 86 deletions(-) diff --git a/Makefile b/Makefile index 51f92aa..26fb8f0 100644 --- a/Makefile +++ b/Makefile @@ -1,6 +1,6 @@ -export GOPATH=$(shell pwd)/GO -export GOBIN=$(GOPATH)/bin -export PATH=$(GOBIN):$(shell echo $${PATH}) +#export GOPATH=$(shell pwd)/GO +#export GOBIN=$(GOPATH)/bin +#export PATH=$(GOBIN):$(shell echo $${PATH}) GOCMD=go GOBUILD=$(GOCMD) build # -compiler gccgo -gccgoflags -O3 @@ -71,4 +71,4 @@ $(foreach P,$(PACKAGE_DIRS),$(eval $(call MAKE_PKG_RULE,$(P)))) $(foreach P,$(OBITOOLS_DIRS),$(eval $(call MAKE_OBITOOLS_RULE,$(P)))) -.PHONY: all packages obitools man obibook doc update-deps \ No newline at end of file +.PHONY: all packages obitools man obibook doc update-deps diff --git a/Release-notes.md b/Release-notes.md index 7317eac..69cf654 100644 --- a/Release-notes.md +++ b/Release-notes.md @@ -2,6 +2,10 @@ ## Latest changes +### New feature +- A new OBITools named `obiscript` allows to process each sequence according to a Lua script. This is + an experimental tool. The **--template** option allows for generating an example script on the `stdout`. + ### API Changes - Two of the main class `obiseq.SeqWorker` and `obiseq.SeqWorker` have their declaration changed. Both now return two values a `obiseq.BioSequenceSlice` and an `error`. This allow a worker to @@ -9,11 +13,14 @@ zero, which is equivalent to filter out the input sequence. ### Enhancement +- In `obitag` if the reference database contains sequences annotated by taxid not referenced in the taxonomy, + the corresponding sequences are discarded from the reference database and a warning indicating the sequence id + and the wrong taxid is emitted. - The bug corrected in the parsing of EMBL and Genbank files as implemented in version 4.1.2 of OBITools4, potentially induced some reduction in the performance of the parsing. This should have been now fixed. - In the same idea, parsing of genbank and EMBL files were reading and storing in memory not only the sequence - but also the annotations (features table). Up to now none of the obitools are using this information, but + but also the annotations (features table). Up to now none of the OBITools are using this information, but with large complete genomes, it is occupying a lot of memory. To reduce this impact, the new version of the parser doesn't any more store in memory the annotations by default. - Add a **--taxonomic-path** to `obiannotate`. The option adds a `taxonomic_path` tag to sequences describing @@ -23,6 +30,10 @@ root of the taxonomy. The latest corresponds to the taxid of the sequence. If a sequence is not annotated by a taxid, as usual the sequence is assumed having the taxid 1 (the root of the taxonomy). +### Bug fixes +- Fix a bug in the parsing of the JSON header of FASTA and FASTQ files occurring when a string includes a curly + brace. + ## February 16th, 2024. Release 4.1.2 ### Bug fixes diff --git a/go.mod b/go.mod index a91c367..9007076 100644 --- a/go.mod +++ b/go.mod @@ -1,6 +1,6 @@ module git.metabarcoding.org/obitools/obitools4/obitools4 -go 1.21 +go 1.22.1 require ( github.com/DavidGamba/go-getoptions v0.28.0 @@ -15,7 +15,7 @@ require ( github.com/sirupsen/logrus v1.9.3 github.com/stretchr/testify v1.7.0 github.com/tevino/abool/v2 v2.1.0 - github.com/traefik/yaegi v0.15.1 + github.com/yuin/gopher-lua v1.1.1 golang.org/x/exp v0.0.0-20231006140011-7918f672742d gonum.org/v1/gonum v0.14.0 gopkg.in/yaml.v3 v3.0.1 @@ -23,22 +23,11 @@ require ( ) require ( - github.com/alecthomas/chroma v0.10.0 // indirect - github.com/alexeyco/binder v0.0.0-20180729220023-2a21303f588a // indirect - github.com/chzyer/readline v1.5.0 // indirect github.com/davecgh/go-spew v1.1.1 // indirect - github.com/dlclark/regexp2 v1.11.0 // indirect - github.com/dop251/goja v0.0.0-20240220182346-e401ed450204 // indirect - github.com/fatih/color v1.16.0 // indirect - github.com/go-sourcemap/sourcemap v2.1.3+incompatible // indirect - github.com/google/pprof v0.0.0-20230207041349-798e818bf904 // indirect github.com/kr/pretty v0.3.0 // indirect github.com/kr/text v0.2.0 // indirect - github.com/mattn/go-colorable v0.1.13 // indirect - github.com/mattn/go-isatty v0.0.20 // indirect github.com/pmezard/go-difflib v1.0.0 // indirect - github.com/yuin/gopher-lua v1.1.1 // indirect - golang.org/x/text v0.13.0 // indirect + github.com/rogpeppe/go-internal v1.6.1 // indirect ) require ( diff --git a/go.sum b/go.sum index 65969e2..7fc23b9 100644 --- a/go.sum +++ b/go.sum @@ -4,48 +4,23 @@ github.com/PaesslerAG/gval v1.2.2 h1:Y7iBzhgE09IGTt5QgGQ2IdaYYYOU134YGHBThD+wm9E github.com/PaesslerAG/gval v1.2.2/go.mod h1:XRFLwvmkTEdYziLdaCeCa5ImcGVrfQbeNUbVR+C6xac= github.com/PaesslerAG/jsonpath v0.1.0 h1:gADYeifvlqK3R3i2cR5B4DGgxLXIPb3TRTH1mGi0jPI= github.com/PaesslerAG/jsonpath v0.1.0/go.mod h1:4BzmtoM/PI8fPO4aQGIusjGxGir2BzcV0grWtFzq1Y8= -github.com/alecthomas/chroma v0.10.0 h1:7XDcGkCQopCNKjZHfYrNLraA+M7e0fMiJ/Mfikbfjek= -github.com/alecthomas/chroma v0.10.0/go.mod h1:jtJATyUxlIORhUOFNA9NZDWGAQ8wpxQQqNSB4rjA/1s= -github.com/alexeyco/binder v0.0.0-20180729220023-2a21303f588a h1:eVFBuipE7TEjIyfrbnQUTG3dBYEtqrRKXSInpyLv41Y= -github.com/alexeyco/binder v0.0.0-20180729220023-2a21303f588a/go.mod h1:uxLp5y9OziDVlIADUk/fpPnEM479nk3gNNZEotIoKoA= github.com/barkimedes/go-deepcopy v0.0.0-20220514131651-17c30cfc62df h1:GSoSVRLoBaFpOOds6QyY1L8AX7uoY+Ln3BHc22W40X0= github.com/barkimedes/go-deepcopy v0.0.0-20220514131651-17c30cfc62df/go.mod h1:hiVxq5OP2bUGBRNS3Z/bt/reCLFNbdcST6gISi1fiOM= github.com/chen3feng/stl4go v0.1.1 h1:0L1+mDw7pomftKDruM23f1mA7miavOj6C6MZeadzN2Q= github.com/chen3feng/stl4go v0.1.1/go.mod h1:5ml3psLgETJjRJnMbPE+JiHLrCpt+Ajc2weeTECXzWU= -github.com/chzyer/logex v1.2.0/go.mod h1:9+9sk7u7pGNWYMkh0hdiL++6OeibzJccyQU4p4MedaY= -github.com/chzyer/readline v1.5.0 h1:lSwwFrbNviGePhkewF1az4oLmcwqCZijQ2/Wi3BGHAI= -github.com/chzyer/readline v1.5.0/go.mod h1:x22KAscuvRqlLoK9CsoYsmxoXZMMFVyOl86cAH8qUic= -github.com/chzyer/test v0.0.0-20210722231415-061457976a23/go.mod h1:Q3SI9o4m/ZMnBNeIyt5eFwwo7qiLfzFZmjNmxjkiQlU= github.com/creack/pty v1.1.9/go.mod h1:oKZEueFk5CKHvIhNR5MUki03XCEU+Q6VDXinZuGJ33E= github.com/daichi-m/go18ds v1.12.1 h1:Pjc3IApmN4qtDiovGP9MvMpIzgZle3SHUcNaA5j46bg= github.com/daichi-m/go18ds v1.12.1/go.mod h1:wc2dURUr8aMxxC4Mn5ObJGVM7uIKU8JagY4nhtonXq8= github.com/davecgh/go-spew v1.1.0/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38= github.com/davecgh/go-spew v1.1.1 h1:vj9j/u1bqnvCEfJOwUhtlOARqs3+rkHYY13jYWTU97c= github.com/davecgh/go-spew v1.1.1/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38= -github.com/dlclark/regexp2 v1.4.0/go.mod h1:2pZnwuY/m+8K6iRw6wQdMtk+rH5tNGR1i55kozfMjCc= -github.com/dlclark/regexp2 v1.4.1-0.20201116162257-a2a8dda75c91/go.mod h1:2pZnwuY/m+8K6iRw6wQdMtk+rH5tNGR1i55kozfMjCc= -github.com/dlclark/regexp2 v1.7.0/go.mod h1:DHkYz0B9wPfa6wondMfaivmHpzrQ3v9q8cnmRbL6yW8= -github.com/dlclark/regexp2 v1.11.0 h1:G/nrcoOa7ZXlpoa/91N3X7mM3r8eIlMBBJZvsz/mxKI= -github.com/dlclark/regexp2 v1.11.0/go.mod h1:DHkYz0B9wPfa6wondMfaivmHpzrQ3v9q8cnmRbL6yW8= -github.com/dop251/goja v0.0.0-20211022113120-dc8c55024d06/go.mod h1:R9ET47fwRVRPZnOGvHxxhuZcbrMCuiqOz3Rlrh4KSnk= -github.com/dop251/goja v0.0.0-20240220182346-e401ed450204 h1:O7I1iuzEA7SG+dK8ocOBSlYAA9jBUmCYl/Qa7ey7JAM= -github.com/dop251/goja v0.0.0-20240220182346-e401ed450204/go.mod h1:QMWlm50DNe14hD7t24KEqZuUdC9sOTy8W6XbCU1mlw4= -github.com/dop251/goja_nodejs v0.0.0-20210225215109-d91c329300e7/go.mod h1:hn7BA7c8pLvoGndExHudxTDKZ84Pyvv+90pbBjbTz0Y= -github.com/dop251/goja_nodejs v0.0.0-20211022123610-8dd9abb0616d/go.mod h1:DngW8aVqWbuLRMHItjPUyqdj+HWPvnQe8V8y1nDpIbM= github.com/dsnet/compress v0.0.1 h1:PlZu0n3Tuv04TzpfPbrnI0HW/YwodEXDS+oPKahKF0Q= github.com/dsnet/compress v0.0.1/go.mod h1:Aw8dCMJ7RioblQeTqt88akK31OvO8Dhf5JflhBbQEHo= github.com/dsnet/golib v0.0.0-20171103203638-1ea166775780/go.mod h1:Lj+Z9rebOhdfkVLjJ8T6VcRQv3SXugXy999NBtR9aFY= -github.com/fatih/color v1.16.0 h1:zmkK9Ngbjj+K0yRhTVONQh1p/HknKYSlNT+vZCzyokM= -github.com/fatih/color v1.16.0/go.mod h1:fL2Sau1YI5c0pdGEVCbKQbLXB6edEj1ZgiY4NijnWvE= github.com/gabriel-vasile/mimetype v1.4.3 h1:in2uUcidCuFcDKtdcBxlR0rJ1+fsokWf+uqxgUFjbI0= github.com/gabriel-vasile/mimetype v1.4.3/go.mod h1:d8uq/6HKRL6CGdk+aubisF/M5GcPfT7nKyLpA0lbSSk= -github.com/go-sourcemap/sourcemap v2.1.3+incompatible h1:W1iEw64niKVGogNgBN3ePyLFfuisuzeidWPMPWmECqU= -github.com/go-sourcemap/sourcemap v2.1.3+incompatible/go.mod h1:F8jJfvm2KbVjc5NqelyYJmf/v5J0dwNLS2mL4sNA1Jg= github.com/goccy/go-json v0.10.2 h1:CrxCmQqYDkv1z7lO7Wbh2HN93uovUHgrECaO5ZrCXAU= github.com/goccy/go-json v0.10.2/go.mod h1:6MelG93GURQebXPDq3khkgXZkazVtN9CRI+MGFi0w8I= -github.com/google/pprof v0.0.0-20230207041349-798e818bf904 h1:4/hN5RUoecvl+RmJRE2YxKWtnnQls6rQjjW5oV7qg2U= -github.com/google/pprof v0.0.0-20230207041349-798e818bf904/go.mod h1:uglQLonpP8qtYCYyzA+8c/9qtqgA3qsXGYqCPKARAFg= -github.com/ianlancetaylor/demangle v0.0.0-20220319035150-800ac71e25c2/go.mod h1:aYm2/VgdVmcIU8iMfdMvDMsRAQjcfZSKFby6HOFvi/w= 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= @@ -54,21 +29,14 @@ github.com/klauspost/cpuid v1.2.0/go.mod h1:Pj4uuM528wm8OyEC2QMXAi2YiTZ96dNQPGgo 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= @@ -79,6 +47,7 @@ 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 h1:/FiVV8dS/e+YqF2JvO3yXRFbBLTIuSDkuC7aBOAvL+k= 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= @@ -94,55 +63,23 @@ github.com/stretchr/testify v1.7.0 h1:nwc3DEeHmmLAfoZucVR881uASk0Mfjw8xYJ99tb5Cc github.com/stretchr/testify v1.7.0/go.mod h1:6Fq8oRcR53rry900zMqJjRRixrwX3KX962/h/Wwjteg= github.com/tevino/abool/v2 v2.1.0 h1:7w+Vf9f/5gmKT4m4qkayb33/92M+Um45F2BkHOR+L/c= github.com/tevino/abool/v2 v2.1.0/go.mod h1:+Lmlqk6bHDWHqN1cbxqhwEAwMPXgc8I1SDEamtseuXY= -github.com/traefik/yaegi v0.15.1 h1:YA5SbaL6HZA0Exh9T/oArRHqGN2HQ+zgmCY7dkoTXu4= -github.com/traefik/yaegi v0.15.1/go.mod h1:AVRxhaI2G+nUsaM1zyktzwXn69G3t/AuTDrCiTds9p0= 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 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