diff --git a/CHANGELOG.md b/CHANGELOG.md index b23307d..246e241 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -20,6 +20,8 @@ - do not append space if there's no description after the sequene ID. - `seqkit sliding`: - new flag `-S/--suffix` for change the suffix added to the sequence ID (default: _sliding). + - `seqkit amplicon`: + - fix BED coordinates for amplicons found in the minus strand. [#367](https://github.com/shenwei356/seqkit/issues/367) - [SeqKit v2.3.1](https://github.com/shenwei356/seqkit/releases/tag/v2.3.1) - 2022-09-22 [![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/seqkit/v2.3.1/total.svg)](https://github.com/shenwei356/seqkit/releases/tag/v2.3.1) - `seqkit grep/locate`: fix bug of FMIndex building for empty sequences. [#321](https://github.com/shenwei356/seqkit/issues/321) diff --git a/doc/docs/usage.md b/doc/docs/usage.md index 34b55cd..6f37417 100644 --- a/doc/docs/usage.md +++ b/doc/docs/usage.md @@ -2114,7 +2114,7 @@ Examples seq1 3 13 p1 0 + CCCACTGAAA seq1 1 7 p4 0 + CGCCCA seq1 3 13 p2 0 - TTTCAGTGGG - seq1 3 6 p3 0 - TTT + seq1 10 13 p3 0 - TTT seq2 1 17 p4 0 + CGTACGGTCAGATCCA seq2 1 15 P5 0 + CGTACGGTCAGATC seq2 3 17 p6 0 + TACGGTCAGATCCA diff --git a/go.mod b/go.mod index 867dd9c..0e1a1eb 100644 --- a/go.mod +++ b/go.mod @@ -5,6 +5,7 @@ go 1.17 require ( github.com/biogo/biogo v1.0.4 github.com/biogo/hts v1.4.4 + github.com/botond-sipos/thist v1.1.0 github.com/cespare/xxhash/v2 v2.1.2 github.com/cznic/sortutil v0.0.0-20181122101858-f5f958428db8 github.com/dustin/go-humanize v1.0.0 @@ -33,15 +34,26 @@ require ( replace github.com/miekg/dns v1.0.14 => github.com/miekg/dns v1.1.46 require ( + git.sr.ht/~sbinet/gg v0.3.1 // indirect + github.com/ajstarks/svgo v0.0.0-20211024235047-1546f124cd8b // indirect github.com/davecgh/go-spew v1.1.1 // indirect github.com/edsrzf/mmap-go v1.1.0 // indirect + github.com/go-fonts/liberation v0.2.0 // indirect + github.com/go-latex/latex v0.0.0-20210823091927-c0d11ff05a81 // indirect + github.com/go-pdf/fpdf v0.6.0 // indirect + github.com/golang/freetype v0.0.0-20170609003504-e2365dfdc4a0 // indirect github.com/inconshreveable/mousetrap v1.0.1 // indirect github.com/mattn/go-runewidth v0.0.14 // indirect github.com/rivo/uniseg v0.4.2 // indirect github.com/rogpeppe/go-internal v1.9.0 // indirect github.com/shenwei356/natsort v0.0.0-20220117010048-580176ad49fb // indirect github.com/spf13/pflag v1.0.5 // indirect + golang.org/x/crypto v0.0.0-20220919173607-35f4265a4bc0 // indirect + golang.org/x/image v0.0.0-20220902085622-e7cb96979f69 // indirect golang.org/x/sys v0.0.0-20220919091848-fb04ddd9f9c8 // indirect + golang.org/x/term v0.0.0-20220919170432-7a66f970e087 // indirect + golang.org/x/text v0.3.7 // indirect + gonum.org/v1/plot v0.12.0 // indirect gopkg.in/yaml.v2 v2.4.0 // indirect gopkg.in/yaml.v3 v3.0.0-20210107192922-496545a6307b // indirect ) diff --git a/go.sum b/go.sum index 196e45b..57195d0 100644 --- a/go.sum +++ b/go.sum @@ -1,5 +1,15 @@ dmitri.shuralyov.com/gpu/mtl v0.0.0-20190408044501-666a987793e9/go.mod h1:H6x//7gZCb22OMCxBHrMx7a5I7Hp++hsVxbQ4BYO7hU= +dmitri.shuralyov.com/gpu/mtl v0.0.0-20201218220906-28db891af037/go.mod h1:H6x//7gZCb22OMCxBHrMx7a5I7Hp++hsVxbQ4BYO7hU= +gioui.org v0.0.0-20210308172011-57750fc8a0a6/go.mod h1:RSH6KIUZ0p2xy5zHDxgAM4zumjgTw83q2ge/PI+yyw8= +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/BurntSushi/toml v0.3.1/go.mod h1:xHWCNGjB5oqiDr8zfno3MHue2Ht5sIBksp03qcyfWMU= github.com/BurntSushi/xgb v0.0.0-20160522181843-27f122750802/go.mod h1:IVnqGOEym/WlBOVXweHU+Q+/VP0lqqI8lqeDx9IjBqo= +github.com/ajstarks/deck v0.0.0-20200831202436-30c9fc6549a9/go.mod h1:JynElWSGnm/4RlzPXRlREEwqTHAN3T56Bv2ITsFT3gY= +github.com/ajstarks/deck/generate v0.0.0-20210309230005-c3f852c02e19/go.mod h1:T13YZdzov6OU0A1+RfKZiZN9ca6VeKdBdyDV+BY97Tk= +github.com/ajstarks/svgo v0.0.0-20180226025133-644b8db467af/go.mod h1:K08gAheRH3/J6wwsYMMT4xOr94bZjxIelGM0+d/wbFw= +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/biogo/biogo v1.0.4 h1:I+FV8WHty5o6pk1VWZxwFETJDcd25GKcGsghMTeQgCY= github.com/biogo/biogo v1.0.4/go.mod h1:WlqzR+oIOt6UKRqDbDsbLm7zHe4+FLLDd9iFTrnfloc= github.com/biogo/boom v0.0.0-20150317015657-28119bc1ffc1 h1:LAHY5JxqhOgJDeDBGKsQ4300qd3sG8C0j5CQS8gD+Kw= @@ -9,6 +19,10 @@ github.com/biogo/hts v1.1.0/go.mod h1:6C9MdMt9ALD5PsluK5n0B0svHOpmVse3UjQQx/cTgO github.com/biogo/hts v1.4.4 h1:Z+TminqAKRE/t6nyy5PwI/DL90kdew4GpghB+QdjjFk= github.com/biogo/hts v1.4.4/go.mod h1:AfPn4uJQ2zxi04Q/4vccdmCX16W+IsHXVguPsdh4HE4= github.com/biogo/store v0.0.0-20200104231603-2c6ad937eb83/go.mod h1:wdbXg77soR6ESRprAMEwAQDFtLT6EAGF5o1GRy0cB5k= +github.com/boombuler/barcode v1.0.0/go.mod h1:paBWMcWSl3LHKBqUq+rly7CNSldXjb2rDl3JlRe0mD8= +github.com/boombuler/barcode v1.0.1/go.mod h1:paBWMcWSl3LHKBqUq+rly7CNSldXjb2rDl3JlRe0mD8= +github.com/botond-sipos/thist v1.1.0 h1:qyeA1ApRa6gi3GX+3b40RIBjcL+Z5NdIJNFoRT3YkIE= +github.com/botond-sipos/thist v1.1.0/go.mod h1:ipLIWUSdMnkmjEzNDsfh2QkC+nV735nTh4w1ZwGF4aM= github.com/cespare/xxhash/v2 v2.1.2 h1:YRXhKfTDauu4ajMg1TPgFO5jnlC2HCbmLXMcTG5cbYE= github.com/cespare/xxhash/v2 v2.1.2/go.mod h1:VGX0DQ3Q6kWi7AoAeZDth3/j3BFtOZR5XLFGgcrjCOs= github.com/cpuguy83/go-md2man/v2 v2.0.2/go.mod h1:tgQtvFlXSQOSOSIRvRPT7W67SCa46tRHOmNcaadrF8o= @@ -22,14 +36,41 @@ github.com/dustin/go-humanize v1.0.0 h1:VSnTsYCnlFHaM2/igO1h6X3HA71jcobQuxemgkq4 github.com/dustin/go-humanize v1.0.0/go.mod h1:HtrtbFcZ19U5GC7JDqmcUSB87Iq5E25KnS6fMYU6eOk= github.com/edsrzf/mmap-go v1.1.0 h1:6EUwBLQ/Mcr1EYLE4Tn1VdW1A4ckqCQWZBw8Hr0kjpQ= github.com/edsrzf/mmap-go v1.1.0/go.mod h1:19H/e8pUPLicwkyNgOykDXkJ9F0MHE+Z52B8EIth78Q= +github.com/fogleman/gg v1.2.1-0.20190220221249-0403632d5b90/go.mod h1:R/bRT+9gY/C5z7JzPU0zXsXHKM4/ayA+zqcVNZzPa1k= +github.com/fogleman/gg v1.3.0/go.mod h1:R/bRT+9gY/C5z7JzPU0zXsXHKM4/ayA+zqcVNZzPa1k= github.com/fsnotify/fsnotify v1.5.4 h1:jRbGcIw6P2Meqdwuo0H1p6JVLbL5DHKAKlYndzMwVZI= github.com/fsnotify/fsnotify v1.5.4/go.mod h1:OVB6XrOHzAwXMpEM7uPOzcehqUV2UqJxmVXmkdnm1bU= +github.com/go-fonts/dejavu v0.1.0 h1:JSajPXURYqpr+Cu8U9bt8K+XcACIHWqWrvWCKyeFmVQ= +github.com/go-fonts/dejavu v0.1.0/go.mod h1:4Wt4I4OU2Nq9asgDCteaAaWZOV24E+0/Pwo0gppep4g= +github.com/go-fonts/latin-modern v0.2.0 h1:5/Tv1Ek/QCr20C6ZOz15vw3g7GELYL98KWr8Hgo+3vk= +github.com/go-fonts/latin-modern v0.2.0/go.mod h1:rQVLdDMK+mK1xscDwsqM5J8U2jrRa3T0ecnM9pNujks= +github.com/go-fonts/liberation v0.1.1/go.mod h1:K6qoJYypsmfVjWg8KOVDQhLc8UDgIK2HYqyqAO9z7GY= +github.com/go-fonts/liberation v0.2.0 h1:jAkAWJP4S+OsrPLZM4/eC9iW7CtHy+HBXrEwZXWo5VM= +github.com/go-fonts/liberation v0.2.0/go.mod h1:K6qoJYypsmfVjWg8KOVDQhLc8UDgIK2HYqyqAO9z7GY= +github.com/go-fonts/stix v0.1.0/go.mod h1:w/c1f0ldAUlJmLBvlbkvVXLAD+tAMqobIIQpmnUIzUY= +github.com/go-gl/glfw v0.0.0-20190409004039-e6da0acd62b1/go.mod h1:vR7hzQXu2zJy9AVAgeJqvqgH9Q5CA+iKCZ2gyEVpxRU= github.com/go-gl/glfw/v3.3/glfw v0.0.0-20191125211704-12ad95a8df72/go.mod h1:tQ2UAYgL5IevRw8kRxooKSPJfGvJ9fJQFa0TUsXzTg8= +github.com/go-gl/glfw/v3.3/glfw v0.0.0-20200222043503-6f7a984d4dc4/go.mod h1:tQ2UAYgL5IevRw8kRxooKSPJfGvJ9fJQFa0TUsXzTg8= +github.com/go-latex/latex v0.0.0-20210118124228-b3d85cf34e07/go.mod h1:CO1AlKB2CSIqUrmQPqA0gdRIlnLEY0gK5JGjh37zN5U= +github.com/go-latex/latex v0.0.0-20210823091927-c0d11ff05a81 h1:6zl3BbBhdnMkpSj2YY30qV3gDcVBGtFgVsV3+/i+mKQ= +github.com/go-latex/latex v0.0.0-20210823091927-c0d11ff05a81/go.mod h1:SX0U8uGpxhq9o2S/CELCSUxEWWAuoCUcVCQWv7G2OCk= +github.com/go-pdf/fpdf v0.5.0/go.mod h1:HzcnA+A23uwogo0tp9yU+l3V+KXhiESpt1PMayhOh5M= +github.com/go-pdf/fpdf v0.6.0 h1:MlgtGIfsdMEEQJr2le6b/HNr1ZlQwxyWr77r2aj2U/8= +github.com/go-pdf/fpdf v0.6.0/go.mod h1:HzcnA+A23uwogo0tp9yU+l3V+KXhiESpt1PMayhOh5M= +github.com/golang/freetype v0.0.0-20170609003504-e2365dfdc4a0 h1:DACJavvAHhabrF08vX0COfcOBJRhZ8lUbR+ZWIs0Y5g= +github.com/golang/freetype v0.0.0-20170609003504-e2365dfdc4a0/go.mod h1:E/TSTwGwJL78qG/PmXZO1EjYhfJinVAhrmmHX6Z8B9k= +github.com/google/go-cmp v0.5.7/go.mod h1:n+brtR0CgQNWTVd5ZUFpTBC8YFBDLK/h/bpaJ8/DtOE= +github.com/google/go-cmp v0.5.8/go.mod h1:17dUlkBOakJ0+DkrSSNjCkIjxS6bF9zb3elmeNGIjoY= github.com/iafan/cwalk v0.0.0-20210125030640-586a8832a711 h1:UnfAf/kLhzHd6UQ6nyum/cCqBImrlrpq8rHLVjaKerA= github.com/iafan/cwalk v0.0.0-20210125030640-586a8832a711/go.mod h1:9NZZY8JKo3RhqKRYhRWMgCO4S4adM76u8w4gGUMnlig= github.com/inconshreveable/mousetrap v1.0.0/go.mod h1:PxqpIevigyE2G7u3NXJIT2ANytuPF1OarO4DADm73n8= github.com/inconshreveable/mousetrap v1.0.1 h1:U3uMjPSQEBMNp1lFxmllqCPM6P5u/Xq7Pgzkat/bFNc= github.com/inconshreveable/mousetrap v1.0.1/go.mod h1:vpF70FUmC8bwa3OWnCshd2FqLfsEA9PFc4w1p2J65bw= +github.com/jezek/xgb v1.0.0/go.mod h1:nrhwO0FX/enq75I7Y7G8iN1ubpSGZEiA3v9e9GyRFlk= +github.com/jung-kurt/gofpdf v1.0.0/go.mod h1:7Id9E/uU8ce6rXgefFLlgrJj/GYY22cpxn+r32jIOes= +github.com/jung-kurt/gofpdf v1.0.3-0.20190309125859-24315acbbda5/go.mod h1:7Id9E/uU8ce6rXgefFLlgrJj/GYY22cpxn+r32jIOes= +github.com/jung-kurt/gofpdf v1.16.2/go.mod h1:1hl7y57EsiPAkLbOwzpzqgx1A30nQCk/YmFV8S2vmK0= +github.com/kisielk/gotool v1.0.0/go.mod h1:XhKaO+MFFWcvkIS/tQcRk01m1F5IRFswLeQ+oQHNcck= github.com/klauspost/compress v1.15.12 h1:YClS/PImqYbn+UILDnqxQCZ3RehC9N318SU3kElDUEM= github.com/klauspost/compress v1.15.12/go.mod h1:QPwzmACJjUTFsnSHH934V6woptycfrDDJnH7hvFVbGM= github.com/klauspost/pgzip v1.2.5 h1:qnWYvvKqedOF2ulHpMG72XQol4ILEJ8k2wwRl/Km8oE= @@ -50,10 +91,16 @@ github.com/mattn/go-runewidth v0.0.14 h1:+xnbZSEeDbOIg5/mE6JF0w6n9duR1l3/WmbinWV github.com/mattn/go-runewidth v0.0.14/go.mod h1:Jdepj2loyihRzMpdS35Xk/zdY8IAYHsh153qUoGf23w= github.com/mitchellh/go-homedir v1.1.0 h1:lukF9ziXFxDFPkA1vsr5zpc1XuPDn/wFntq5mG+4E0Y= github.com/mitchellh/go-homedir v1.1.0/go.mod h1:SfyaCUpYCn1Vlf4IUYiD9fPX4A5wJrkLzIz1N1q0pr0= +github.com/phpdave11/gofpdf v1.4.2/go.mod h1:zpO6xFn9yxo3YLyMvW8HcKWVdbNqgIfOOp2dXMnm1mY= +github.com/phpdave11/gofpdi v1.0.7/go.mod h1:vBmVV0Do6hSBHC8uKUQ71JGW+ZGQq74llk/7bXwjDoI= +github.com/phpdave11/gofpdi v1.0.12/go.mod h1:vBmVV0Do6hSBHC8uKUQ71JGW+ZGQq74llk/7bXwjDoI= +github.com/phpdave11/gofpdi v1.0.13/go.mod h1:vBmVV0Do6hSBHC8uKUQ71JGW+ZGQq74llk/7bXwjDoI= +github.com/pkg/errors v0.8.1/go.mod h1:bwawxfHBFNV+L2hUp1rHADufV3IMtnDRdf1r5NINEl0= github.com/pkg/errors v0.9.1 h1:FEBLx1zS214owpjy7qsBeixbURkuhQAwrK5UwLGTwt4= github.com/pkg/errors v0.9.1/go.mod h1:bwawxfHBFNV+L2hUp1rHADufV3IMtnDRdf1r5NINEl0= github.com/pmezard/go-difflib v1.0.0 h1:4DBwDE0NGyQoBHbLQYPwSUPoCMWR5BEzIk/f1lZbAQM= github.com/pmezard/go-difflib v1.0.0/go.mod h1:iKH77koFhYxTK1pcRnkKkqfTogsbg7gZNVY4sRDYZ/4= +github.com/remyoudompheng/bigfft v0.0.0-20170806203942-52369c62f446/go.mod h1:uYEyJGbgTkfkS4+E/PavXkNJcbFIpEtjt2B0KDQ5+9M= github.com/remyoudompheng/bigfft v0.0.0-20200410134404-eec4a21b6bb0 h1:OdAsTTz6OkFY5QxjkYwrChwuRruF69c169dPK26NUlk= github.com/rivo/uniseg v0.2.0/go.mod h1:J6wj4VEh+S6ZtnVlnTBMWIodfgj8LQOQFoIToxlJtxc= github.com/rivo/uniseg v0.4.2 h1:YwD0ulJSJytLpiaWua0sBDusfsCZohxjxzVTYjwxfV8= @@ -61,6 +108,8 @@ github.com/rivo/uniseg v0.4.2/go.mod h1:FN3SvrM+Zdj16jyLfmOkMNblXMcoc8DfTHruCPUc github.com/rogpeppe/go-internal v1.9.0 h1:73kH8U+JUqXU8lRuOHeVHaa/SZPifC7BkcraZVejAe8= github.com/rogpeppe/go-internal v1.9.0/go.mod h1:WtVeX8xhTBvf0smdhujwtBcq4Qrzq/fJaraNFVN+nFs= github.com/russross/blackfriday/v2 v2.1.0/go.mod h1:+Rmxgy9KzJVeS9/2gXHxylqXiyQDYRxCVz55jmeOWTM= +github.com/ruudk/golang-pdf417 v0.0.0-20181029194003-1af4ab5afa58/go.mod h1:6lfFZQK844Gfx8o5WFuvpxWRwnSoipWe/p622j1v06w= +github.com/ruudk/golang-pdf417 v0.0.0-20201230142125-a7e3863a1245/go.mod h1:pQAZKsJ8yyVxGRWYNEm9oFB8ieLgKFnamEyDmSA0BRk= github.com/shenwei356/bio v0.8.4 h1:cLSbMUNHQfx/RuJyMiJs3d7Fmu/vpXYC01oqrFGOSoM= github.com/shenwei356/bio v0.8.4/go.mod h1:47qBrYHaD3vIyFZsbgg8Yz4UnjLhn4dWujCUCTudiVY= github.com/shenwei356/breader v0.3.2 h1:GLy2clIMck6FdTwj8WLnmhv0PW/7Pp+Wcx7TVEHG0ks= @@ -82,6 +131,7 @@ github.com/spf13/cobra v1.5.0/go.mod h1:dWXEIy2H428czQCjInthrTRUg7yKbok+2Qi/yBIJ github.com/spf13/pflag v1.0.5 h1:iy+VFUOCP1a+8yFto/drg2CJ5u0yRoB7fZw3DKv/JXA= github.com/spf13/pflag v1.0.5/go.mod h1:McXfInJRrz4CZXVZOBLb0bTZqETkiAhM9Iw0y3An2Bg= github.com/stretchr/objx v0.1.0/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME= +github.com/stretchr/testify v1.2.2/go.mod h1:a8OnRcib4nhh0OaRAV+Yts87kKdq0PP7pXfy6kDkUVs= github.com/stretchr/testify v1.7.0 h1:nwc3DEeHmmLAfoZucVR881uASk0Mfjw8xYJ99tb5CcY= github.com/stretchr/testify v1.7.0/go.mod h1:6Fq8oRcR53rry900zMqJjRRixrwX3KX962/h/Wwjteg= github.com/tatsushid/go-prettytable v0.0.0-20141013043238-ed2d14c29939 h1:BhIUXV2ySTLrKgh/Hnts+QTQlIbWtomXt3LMdzME0A0= @@ -91,27 +141,117 @@ github.com/twotwotwo/sorts v0.0.0-20160814051341-bf5c1f2b8553/go.mod h1:Rj7Csq/t github.com/ulikunitz/xz v0.5.6/go.mod h1:2bypXElzHzzJZwzH67Y6wb67pO62Rzfn7BSiF4ABRW8= github.com/ulikunitz/xz v0.5.10 h1:t92gobL9l3HE202wg3rlk19F6X+JOxl9BBrCCMYEYd8= github.com/ulikunitz/xz v0.5.10/go.mod h1:nbz6k7qbPmH4IRqmfOplQw/tblSgqTqBwxkY0oWt/14= 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h1:Hei/4ADfdWqJk1ZMxUNpqntNwaWcugrBjAiHlqqRiVk= @@ -120,3 +260,11 @@ 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 v3.0.0-20210107192922-496545a6307b h1:h8qDotaEPuJATrMmW04NCwg7v22aHH28wwpauUhK9Oo= gopkg.in/yaml.v3 v3.0.0-20210107192922-496545a6307b/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM= +honnef.co/go/tools v0.1.3/go.mod h1:NgwopIslSNH47DimFoV78dnkksY2EFtX0ajyb3K/las= +modernc.org/cc v1.0.0/go.mod h1:1Sk4//wdnYJiUIxnW8ddKpaOJCF37yAdqYnkxUpaYxw= +modernc.org/golex v1.0.0/go.mod h1:b/QX9oBD/LhixY6NDh+IdGv17hgB+51fET1i2kPSmvk= +modernc.org/mathutil v1.0.0/go.mod h1:wU0vUrJsVWBZ4P6e7xtFJEhFSNsfRLJ8H458uRjg03k= +modernc.org/strutil v1.0.0/go.mod h1:lstksw84oURvj9y3tn8lGvRxyRC1S2+g5uuIzNfIOBs= +modernc.org/xc v1.0.0/go.mod h1:mRNCo0bvLjGhHO9WsyuKVU4q0ceiDDDoEeWDJHrNx8I= +rsc.io/pdf v0.1.1 h1:k1MczvYDUvJBe93bYd7wrZLLUEcLZAuF824/I4e5Xr4= +rsc.io/pdf v0.1.1/go.mod h1:n8OzWcQ6Sp37PL01nO98y4iUCRdTGarVfzxY20ICaU4= diff --git a/seqkit/cmd/amplicon.go b/seqkit/cmd/amplicon.go index 5298cef..a2ec14d 100644 --- a/seqkit/cmd/amplicon.go +++ b/seqkit/cmd/amplicon.go @@ -310,6 +310,7 @@ Examples: var strand string var tmpSeq *seq.Seq var primer [3][]byte + var start1, end1 int results := make([]string, 0, 2) var s []byte @@ -339,12 +340,16 @@ Examples: } if outFmtBED { + start1, end1 = loc[0]-1, loc[1] + if strand == "-" { + start1, end1 = len(record.Seq.Seq)-loc[1], len(record.Seq.Seq)-loc[0]+1 + } if outputMismatches { s = record.Seq.SubSeq(loc[0], loc[1]).Seq results = append(results, fmt.Sprintf("%s\t%d\t%d\t%s\t%d\t%s\t%s\t%d\t%d\t%d\n", record.ID, - loc[0]-1, - loc[1], + start1, + end1, primer[0], 0, strand, @@ -356,8 +361,8 @@ Examples: } else { results = append(results, fmt.Sprintf("%s\t%d\t%d\t%s\t%d\t%s\t%s\n", record.ID, - loc[0]-1, - loc[1], + start1, + end1, primer[0], 0, strand, @@ -416,6 +421,7 @@ Examples: var primer [3][]byte var matched bool var name0 string + var start1, end1 int for _, file := range files { fastxReader, err = fastx.NewReader(alphabet, file, idRegexp) @@ -464,12 +470,16 @@ Examples: matched = true if outFmtBED { + start1, end1 = loc[0]-1, loc[1] + if strand == "-" { + start1, end1 = len(record.Seq.Seq)-loc[1], len(record.Seq.Seq)-loc[0]+1 + } if outputMismatches { fmt.Fprintf(outfh, "%s\t%d\t%d\t%s\t%d\t%s\t%s\t%d\t%d\t%d\n", record.ID, - loc[0]-1, - loc[1], + start1, + end1, primer[0], 0, strand, @@ -482,8 +492,8 @@ Examples: fmt.Fprintf(outfh, "%s\t%d\t%d\t%s\t%d\t%s\t%s\n", record.ID, - loc[0]-1, - loc[1], + start1, + end1, primer[0], 0, strand, @@ -713,21 +723,20 @@ func (finder *AmpliconFinder) LocateRange(begin, end int, flanking bool, strictM // end: relative location to 3' end of amplicon. // Returned locations are 1-based. // -// F -// -----===============----- -// 1 3 5 x/y -// -5-3-1 x/y -// F R -// -----=====-----=====----- x:y -// -// =============== 1:-1 -// ======= 1:7 -// ===== 3:7 -// ===== 6:10 -// ===== -10:-6 -// ===== -7:-3 -// -x:y (invalid) +// F +// -----===============----- +// 1 3 5 x/y +// -5-3-1 x/y +// F R +// -----=====-----=====----- x:y // +// =============== 1:-1 +// ======= 1:7 +// ===== 3:7 +// ===== 6:10 +// ===== -10:-6 +// ===== -7:-3 +// -x:y (invalid) func SubLocationInner(length, B, E, begin, end int, strictMode bool) (int, int, bool) { if begin == 0 || end == 0 { return 0, 0, false @@ -790,20 +799,19 @@ func SubLocationInner(length, B, E, begin, end int, strictMode bool) (int, int, // end: relative location to 3' end of amplicon. // Returned locations are 1-based. // -// F -// -----===============----- -// -3-1 x/y -// 1 3 5 x/y -// F R -// -----=====-----=====----- -// ===== -5:-1 -// === -5:-3 -// ===== 1:5 -// === 3:5 -// ================= -1:1 -// ========================= -5:5 -// x:-y (invalid) -// +// F +// -----===============----- +// -3-1 x/y +// 1 3 5 x/y +// F R +// -----=====-----=====----- +// ===== -5:-1 +// === -5:-3 +// ===== 1:5 +// === 3:5 +// ================= -1:1 +// ========================= -5:5 +// x:-y (invalid) func SubLocationFlanking(length, B, E, begin, end int, strictMode bool) (int, int, bool) { if begin == 0 || end == 0 { return 0, 0, false