├── offtarget_info └── test.txt ├── exonerate ├── exonerate_macos │ ├── info │ │ ├── git │ │ ├── hash_input.json │ │ ├── test │ │ │ └── run_test.sh │ │ ├── index.json │ │ ├── files │ │ ├── recipe │ │ │ ├── build.sh │ │ │ ├── meta.yaml.template │ │ │ ├── meta.yaml │ │ │ └── conda_build_config.yaml │ │ ├── about.json │ │ ├── has_prefix │ │ └── paths.json │ ├── .DS_Store │ ├── bin │ │ ├── esd2esi │ │ ├── ipcress │ │ ├── exonerate │ │ ├── fasta2esd │ │ ├── fastaclean │ │ ├── fastaclip │ │ ├── fastadiff │ │ ├── fastafetch │ │ ├── fastaindex │ │ ├── fastanrdb │ │ ├── fastasort │ │ ├── fastasplit │ │ ├── fastachecksum │ │ ├── fastaexplode │ │ ├── fastahardmask │ │ ├── fastalength │ │ ├── fastaoverlap │ │ ├── fastareformat │ │ ├── fastaremove │ │ ├── fastarevcomp │ │ ├── fastasoftmask │ │ ├── fastasubseq │ │ ├── fastavalidcds │ │ ├── fastatranslate │ │ ├── exonerate-server │ │ ├── fastaannotatecdna │ │ └── fastacomposition │ └── share │ │ └── man │ │ └── man1 │ │ ├── fastautils.1 │ │ ├── ipcress.1 │ │ └── exonerate-server.1 ├── .DS_Store ├── exonerate_win │ ├── .DS_Store │ └── bin │ │ ├── cygwin1.dll │ │ ├── cyggcc_s-1.dll │ │ ├── cygiconv-2.dll │ │ ├── cygintl-8.dll │ │ ├── cygpcre-1.dll │ │ ├── exonerate.exe │ │ └── cygglib-2.0-0.dll └── exonerate_linux │ ├── .DS_Store │ ├── bin │ ├── esd2esi │ ├── ipcress │ ├── exonerate │ ├── fasta2esd │ ├── fastaclean │ ├── fastaclip │ ├── fastadiff │ ├── fastafetch │ ├── fastaindex │ ├── fastanrdb │ ├── fastasort │ ├── fastasplit │ ├── fastachecksum │ ├── fastaexplode │ ├── fastahardmask │ ├── fastalength │ ├── fastaoverlap │ ├── fastareformat │ ├── fastaremove │ ├── fastarevcomp │ ├── fastasoftmask │ ├── fastasubseq │ ├── fastavalidcds │ ├── fastatranslate │ ├── exonerate-server │ ├── fastaannotatecdna │ └── fastacomposition │ └── share │ └── man │ └── man1 │ ├── fastautils.1 │ ├── ipcress.1 │ └── exonerate-server.1 ├── .DS_Store ├── statics ├── .DS_Store ├── img │ ├── 1.png │ ├── 2.png │ ├── file.png │ └── photo.png ├── font-awesome-4.7.0 │ ├── .DS_Store │ ├── fonts │ │ ├── FontAwesome.otf │ │ ├── fontawesome-webfont.eot │ │ ├── fontawesome-webfont.ttf │ │ ├── fontawesome-webfont.woff │ │ └── fontawesome-webfont.woff2 │ ├── less │ │ ├── screen-reader.less │ │ ├── fixed-width.less │ │ ├── larger.less │ │ ├── list.less │ │ ├── core.less │ │ ├── stacked.less │ │ ├── font-awesome.less │ │ ├── bordered-pulled.less │ │ ├── rotated-flipped.less │ │ ├── path.less │ │ ├── animated.less │ │ └── mixins.less │ ├── scss │ │ ├── _fixed-width.scss │ │ ├── _screen-reader.scss │ │ ├── _larger.scss │ │ ├── _list.scss │ │ ├── _core.scss │ │ ├── font-awesome.scss │ │ ├── _stacked.scss │ │ ├── _bordered-pulled.scss │ │ ├── _rotated-flipped.scss │ │ ├── _path.scss │ │ ├── _animated.scss │ │ └── _mixins.scss │ └── HELP-US-OUT.txt ├── css │ └── main.css └── js │ ├── result.js │ └── main.js ├── protein.fa ├── README.md ├── LICENSE ├── package.json ├── cds.fa ├── codon_info.json ├── dna.fa ├── result.html ├── .gitignore ├── overlap_info.json └── index.html /offtarget_info/test.txt: -------------------------------------------------------------------------------- 1 | test text -------------------------------------------------------------------------------- /exonerate/exonerate_macos/info/git: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zhangtaolab/CRISPR-BETS_desktop/main/.DS_Store -------------------------------------------------------------------------------- /statics/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zhangtaolab/CRISPR-BETS_desktop/main/statics/.DS_Store -------------------------------------------------------------------------------- /statics/img/1.png: 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-------------------------------------------------------------------------------- /statics/font-awesome-4.7.0/fonts/fontawesome-webfont.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zhangtaolab/CRISPR-BETS_desktop/main/statics/font-awesome-4.7.0/fonts/fontawesome-webfont.woff2 -------------------------------------------------------------------------------- /statics/font-awesome-4.7.0/less/screen-reader.less: -------------------------------------------------------------------------------- 1 | // Screen Readers 2 | // ------------------------- 3 | 4 | .sr-only { .sr-only(); } 5 | .sr-only-focusable { .sr-only-focusable(); } 6 | -------------------------------------------------------------------------------- /statics/font-awesome-4.7.0/less/fixed-width.less: -------------------------------------------------------------------------------- 1 | // Fixed Width Icons 2 | // ------------------------- 3 | .@{fa-css-prefix}-fw { 4 | width: (18em / 14); 5 | text-align: center; 6 | } 7 | -------------------------------------------------------------------------------- /statics/font-awesome-4.7.0/scss/_fixed-width.scss: -------------------------------------------------------------------------------- 1 | // Fixed Width Icons 2 | // ------------------------- 3 | .#{$fa-css-prefix}-fw { 4 | width: (18em / 14); 5 | text-align: center; 6 | } 7 | -------------------------------------------------------------------------------- /protein.fa: -------------------------------------------------------------------------------- 1 | >protein 2 | MAGSGRDRDPLVVGRVVGDVLDAFVRSTNLKVTYGSKTVSNGCELKPSMVTHQPRVEVGGNDMRTFYTLVMVDPDAPSPSDPNLREYLHWLVTDIPGTTAASFGQEVMCYESPRPTMGIHRLVFVLFQQLGRQTVYAPGWRQNFNTKDFAELYNLGSPVAAVYFNCQREAGSGGRRVYP* -------------------------------------------------------------------------------- /statics/font-awesome-4.7.0/scss/_screen-reader.scss: -------------------------------------------------------------------------------- 1 | // Screen Readers 2 | // ------------------------- 3 | 4 | .sr-only { @include sr-only(); } 5 | .sr-only-focusable { @include sr-only-focusable(); } 6 | -------------------------------------------------------------------------------- /statics/font-awesome-4.7.0/HELP-US-OUT.txt: -------------------------------------------------------------------------------- 1 | I hope you love Font Awesome. If you've found it useful, please do me a favor and check out my latest project, 2 | Fort Awesome (https://fortawesome.com). It makes it easy to put the perfect icons on your website. Choose from our awesome, 3 | comprehensive icon sets or copy and paste your own. 4 | 5 | Please. Check it out. 6 | 7 | -Dave Gandy 8 | -------------------------------------------------------------------------------- /exonerate/exonerate_macos/info/index.json: -------------------------------------------------------------------------------- 1 | { 2 | "arch": "x86_64", 3 | "build": "hbe7ca29_3", 4 | "build_number": 3, 5 | "depends": [ 6 | "glib >=2.58.3,<3.0a0", 7 | "pcre >=8.43,<9.0a0" 8 | ], 9 | "license": "GPL-3.0", 10 | "name": "exonerate", 11 | "platform": "osx", 12 | "subdir": "osx-64", 13 | "timestamp": 1572344210060, 14 | "version": "2.4.0" 15 | } -------------------------------------------------------------------------------- /statics/font-awesome-4.7.0/less/larger.less: -------------------------------------------------------------------------------- 1 | // Icon Sizes 2 | // ------------------------- 3 | 4 | /* makes the font 33% larger relative to the icon container */ 5 | .@{fa-css-prefix}-lg { 6 | font-size: (4em / 3); 7 | line-height: (3em / 4); 8 | vertical-align: -15%; 9 | } 10 | .@{fa-css-prefix}-2x { font-size: 2em; } 11 | .@{fa-css-prefix}-3x { font-size: 3em; } 12 | .@{fa-css-prefix}-4x { font-size: 4em; } 13 | .@{fa-css-prefix}-5x { font-size: 5em; } 14 | -------------------------------------------------------------------------------- /statics/font-awesome-4.7.0/scss/_larger.scss: -------------------------------------------------------------------------------- 1 | // Icon Sizes 2 | // ------------------------- 3 | 4 | /* makes the font 33% larger relative to the icon container */ 5 | .#{$fa-css-prefix}-lg { 6 | font-size: (4em / 3); 7 | line-height: (3em / 4); 8 | vertical-align: -15%; 9 | } 10 | .#{$fa-css-prefix}-2x { font-size: 2em; } 11 | .#{$fa-css-prefix}-3x { font-size: 3em; } 12 | .#{$fa-css-prefix}-4x { font-size: 4em; } 13 | .#{$fa-css-prefix}-5x { font-size: 5em; } 14 | -------------------------------------------------------------------------------- /statics/font-awesome-4.7.0/less/list.less: -------------------------------------------------------------------------------- 1 | // List Icons 2 | // ------------------------- 3 | 4 | .@{fa-css-prefix}-ul { 5 | padding-left: 0; 6 | margin-left: @fa-li-width; 7 | list-style-type: none; 8 | > li { position: relative; } 9 | } 10 | .@{fa-css-prefix}-li { 11 | position: absolute; 12 | left: -@fa-li-width; 13 | width: @fa-li-width; 14 | top: (2em / 14); 15 | text-align: center; 16 | &.@{fa-css-prefix}-lg { 17 | left: (-@fa-li-width + (4em / 14)); 18 | } 19 | } 20 | -------------------------------------------------------------------------------- /statics/font-awesome-4.7.0/scss/_list.scss: -------------------------------------------------------------------------------- 1 | // List Icons 2 | // ------------------------- 3 | 4 | .#{$fa-css-prefix}-ul { 5 | padding-left: 0; 6 | margin-left: $fa-li-width; 7 | list-style-type: none; 8 | > li { position: relative; } 9 | } 10 | .#{$fa-css-prefix}-li { 11 | position: absolute; 12 | left: -$fa-li-width; 13 | width: $fa-li-width; 14 | top: (2em / 14); 15 | text-align: center; 16 | &.#{$fa-css-prefix}-lg { 17 | left: -$fa-li-width + (4em / 14); 18 | } 19 | } 20 | -------------------------------------------------------------------------------- /statics/font-awesome-4.7.0/less/core.less: -------------------------------------------------------------------------------- 1 | // Base Class Definition 2 | // ------------------------- 3 | 4 | .@{fa-css-prefix} { 5 | display: inline-block; 6 | font: normal normal normal @fa-font-size-base/@fa-line-height-base FontAwesome; // shortening font declaration 7 | font-size: inherit; // can't have font-size inherit on line above, so need to override 8 | text-rendering: auto; // optimizelegibility throws things off #1094 9 | -webkit-font-smoothing: antialiased; 10 | -moz-osx-font-smoothing: grayscale; 11 | 12 | } 13 | -------------------------------------------------------------------------------- /statics/font-awesome-4.7.0/scss/_core.scss: -------------------------------------------------------------------------------- 1 | // Base Class Definition 2 | // ------------------------- 3 | 4 | .#{$fa-css-prefix} { 5 | display: inline-block; 6 | font: normal normal normal #{$fa-font-size-base}/#{$fa-line-height-base} FontAwesome; // shortening font declaration 7 | font-size: inherit; // can't have font-size inherit on line above, so need to override 8 | text-rendering: auto; // optimizelegibility throws things off #1094 9 | -webkit-font-smoothing: antialiased; 10 | -moz-osx-font-smoothing: grayscale; 11 | 12 | } 13 | -------------------------------------------------------------------------------- /statics/font-awesome-4.7.0/scss/font-awesome.scss: -------------------------------------------------------------------------------- 1 | /*! 2 | * Font Awesome 4.7.0 by @davegandy - http://fontawesome.io - @fontawesome 3 | * License - http://fontawesome.io/license (Font: SIL OFL 1.1, CSS: MIT License) 4 | */ 5 | 6 | @import "variables"; 7 | @import "mixins"; 8 | @import "path"; 9 | @import "core"; 10 | @import "larger"; 11 | @import "fixed-width"; 12 | @import "list"; 13 | @import "bordered-pulled"; 14 | @import "animated"; 15 | @import "rotated-flipped"; 16 | @import "stacked"; 17 | @import "icons"; 18 | @import "screen-reader"; 19 | -------------------------------------------------------------------------------- /statics/font-awesome-4.7.0/less/stacked.less: -------------------------------------------------------------------------------- 1 | // Stacked Icons 2 | // ------------------------- 3 | 4 | .@{fa-css-prefix}-stack { 5 | position: relative; 6 | display: inline-block; 7 | width: 2em; 8 | height: 2em; 9 | line-height: 2em; 10 | vertical-align: middle; 11 | } 12 | .@{fa-css-prefix}-stack-1x, .@{fa-css-prefix}-stack-2x { 13 | position: absolute; 14 | left: 0; 15 | width: 100%; 16 | text-align: center; 17 | } 18 | .@{fa-css-prefix}-stack-1x { line-height: inherit; } 19 | .@{fa-css-prefix}-stack-2x { font-size: 2em; } 20 | .@{fa-css-prefix}-inverse { color: @fa-inverse; } 21 | -------------------------------------------------------------------------------- /statics/font-awesome-4.7.0/scss/_stacked.scss: -------------------------------------------------------------------------------- 1 | // Stacked Icons 2 | // ------------------------- 3 | 4 | .#{$fa-css-prefix}-stack { 5 | position: relative; 6 | display: inline-block; 7 | width: 2em; 8 | height: 2em; 9 | line-height: 2em; 10 | vertical-align: middle; 11 | } 12 | .#{$fa-css-prefix}-stack-1x, .#{$fa-css-prefix}-stack-2x { 13 | position: absolute; 14 | left: 0; 15 | width: 100%; 16 | text-align: center; 17 | } 18 | .#{$fa-css-prefix}-stack-1x { line-height: inherit; } 19 | .#{$fa-css-prefix}-stack-2x { font-size: 2em; } 20 | .#{$fa-css-prefix}-inverse { color: $fa-inverse; } 21 | -------------------------------------------------------------------------------- /statics/font-awesome-4.7.0/less/font-awesome.less: -------------------------------------------------------------------------------- 1 | /*! 2 | * Font Awesome 4.7.0 by @davegandy - http://fontawesome.io - @fontawesome 3 | * License - http://fontawesome.io/license (Font: SIL OFL 1.1, CSS: MIT License) 4 | */ 5 | 6 | @import "variables.less"; 7 | @import "mixins.less"; 8 | @import "path.less"; 9 | @import "core.less"; 10 | @import "larger.less"; 11 | @import "fixed-width.less"; 12 | @import "list.less"; 13 | @import "bordered-pulled.less"; 14 | @import "animated.less"; 15 | @import "rotated-flipped.less"; 16 | @import "stacked.less"; 17 | @import "icons.less"; 18 | @import "screen-reader.less"; 19 | -------------------------------------------------------------------------------- /statics/css/main.css: -------------------------------------------------------------------------------- 1 | /*body{*/ 2 | /* background-color: rgba(74, 112, 139, 0.1);*/ 3 | /*}*/ 4 | 5 | 6 | .border-radius{ 7 | margin-left: 10px; 8 | margin-right: 10px; 9 | background-color: #0D3349; 10 | border-radius: 8px; 11 | } 12 | 13 | .border-radius a{ 14 | color: #FFFFFF ; 15 | } 16 | 17 | nav a{ 18 | color: #FFFFFF !important; 19 | } 20 | 21 | .border-radius a span{ 22 | margin-right: 5px; 23 | } 24 | 25 | .input-group-append span{ 26 | margin-right: 5px; 27 | } 28 | 29 | .file-type{ 30 | margin-top: 20px; 31 | } 32 | 33 | .title{ 34 | margin-top: 10px; 35 | } 36 | 37 | -------------------------------------------------------------------------------- /exonerate/exonerate_macos/info/files: -------------------------------------------------------------------------------- 1 | bin/esd2esi 2 | bin/exonerate 3 | bin/exonerate-server 4 | bin/fasta2esd 5 | bin/fastaannotatecdna 6 | bin/fastachecksum 7 | bin/fastaclean 8 | bin/fastaclip 9 | bin/fastacomposition 10 | bin/fastadiff 11 | bin/fastaexplode 12 | bin/fastafetch 13 | bin/fastahardmask 14 | bin/fastaindex 15 | bin/fastalength 16 | bin/fastanrdb 17 | bin/fastaoverlap 18 | bin/fastareformat 19 | bin/fastaremove 20 | bin/fastarevcomp 21 | bin/fastasoftmask 22 | bin/fastasort 23 | bin/fastasplit 24 | bin/fastasubseq 25 | bin/fastatranslate 26 | bin/fastavalidcds 27 | bin/ipcress 28 | share/man/man1/exonerate-server.1 29 | share/man/man1/exonerate.1 30 | share/man/man1/fastautils.1 31 | share/man/man1/ipcress.1 32 | -------------------------------------------------------------------------------- /statics/font-awesome-4.7.0/less/bordered-pulled.less: -------------------------------------------------------------------------------- 1 | // Bordered & Pulled 2 | // ------------------------- 3 | 4 | .@{fa-css-prefix}-border { 5 | padding: .2em .25em .15em; 6 | border: solid .08em @fa-border-color; 7 | border-radius: .1em; 8 | } 9 | 10 | .@{fa-css-prefix}-pull-left { float: left; } 11 | .@{fa-css-prefix}-pull-right { float: right; } 12 | 13 | .@{fa-css-prefix} { 14 | &.@{fa-css-prefix}-pull-left { margin-right: .3em; } 15 | &.@{fa-css-prefix}-pull-right { margin-left: .3em; } 16 | } 17 | 18 | /* Deprecated as of 4.4.0 */ 19 | .pull-right { float: right; } 20 | .pull-left { float: left; } 21 | 22 | .@{fa-css-prefix} { 23 | &.pull-left { margin-right: .3em; } 24 | &.pull-right { margin-left: .3em; } 25 | } 26 | -------------------------------------------------------------------------------- /statics/font-awesome-4.7.0/scss/_bordered-pulled.scss: -------------------------------------------------------------------------------- 1 | // Bordered & Pulled 2 | // ------------------------- 3 | 4 | .#{$fa-css-prefix}-border { 5 | padding: .2em .25em .15em; 6 | border: solid .08em $fa-border-color; 7 | border-radius: .1em; 8 | } 9 | 10 | .#{$fa-css-prefix}-pull-left { float: left; } 11 | .#{$fa-css-prefix}-pull-right { float: right; } 12 | 13 | .#{$fa-css-prefix} { 14 | &.#{$fa-css-prefix}-pull-left { margin-right: .3em; } 15 | &.#{$fa-css-prefix}-pull-right { margin-left: .3em; } 16 | } 17 | 18 | /* Deprecated as of 4.4.0 */ 19 | .pull-right { float: right; } 20 | .pull-left { float: left; } 21 | 22 | .#{$fa-css-prefix} { 23 | &.pull-left { margin-right: .3em; } 24 | &.pull-right { margin-left: .3em; } 25 | } 26 | -------------------------------------------------------------------------------- /statics/font-awesome-4.7.0/less/rotated-flipped.less: -------------------------------------------------------------------------------- 1 | // Rotated & Flipped Icons 2 | // ------------------------- 3 | 4 | .@{fa-css-prefix}-rotate-90 { .fa-icon-rotate(90deg, 1); } 5 | .@{fa-css-prefix}-rotate-180 { .fa-icon-rotate(180deg, 2); } 6 | .@{fa-css-prefix}-rotate-270 { .fa-icon-rotate(270deg, 3); } 7 | 8 | .@{fa-css-prefix}-flip-horizontal { .fa-icon-flip(-1, 1, 0); } 9 | .@{fa-css-prefix}-flip-vertical { .fa-icon-flip(1, -1, 2); } 10 | 11 | // Hook for IE8-9 12 | // ------------------------- 13 | 14 | :root .@{fa-css-prefix}-rotate-90, 15 | :root .@{fa-css-prefix}-rotate-180, 16 | :root .@{fa-css-prefix}-rotate-270, 17 | :root .@{fa-css-prefix}-flip-horizontal, 18 | :root .@{fa-css-prefix}-flip-vertical { 19 | filter: none; 20 | } 21 | -------------------------------------------------------------------------------- /exonerate/exonerate_macos/info/recipe/build.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | mkdir -p ${PREFIX}/bin 3 | 4 | export CFLAGS="-I$PREFIX/include" 5 | export LDFLAGS="-L$PREFIX/lib -Wl,-rpath ${PREFIX}/lib" 6 | export CPATH=${PREFIX}/include 7 | 8 | if [[ "$(uname)" == Darwin ]]; then 9 | # Fix for install_name_tool error: 10 | # error: install_name_tool: changing install names or rpaths can't be 11 | # redone for: ... (for architecture x86_64) because 12 | # larger updated load commands do not fit (the program must be relinked, 13 | # and you may need to use -headerpad or -headerpad_max_install_names) 14 | export LDFLAGS="$LDFLAGS -headerpad_max_install_names" 15 | fi 16 | 17 | ./configure --prefix=${PREFIX} --enable-pthreads 18 | make 19 | make install 20 | -------------------------------------------------------------------------------- /statics/font-awesome-4.7.0/scss/_rotated-flipped.scss: -------------------------------------------------------------------------------- 1 | // Rotated & Flipped Icons 2 | // ------------------------- 3 | 4 | .#{$fa-css-prefix}-rotate-90 { @include fa-icon-rotate(90deg, 1); } 5 | .#{$fa-css-prefix}-rotate-180 { @include fa-icon-rotate(180deg, 2); } 6 | .#{$fa-css-prefix}-rotate-270 { @include fa-icon-rotate(270deg, 3); } 7 | 8 | .#{$fa-css-prefix}-flip-horizontal { @include fa-icon-flip(-1, 1, 0); } 9 | .#{$fa-css-prefix}-flip-vertical { @include fa-icon-flip(1, -1, 2); } 10 | 11 | // Hook for IE8-9 12 | // ------------------------- 13 | 14 | :root .#{$fa-css-prefix}-rotate-90, 15 | :root .#{$fa-css-prefix}-rotate-180, 16 | :root .#{$fa-css-prefix}-rotate-270, 17 | :root .#{$fa-css-prefix}-flip-horizontal, 18 | :root .#{$fa-css-prefix}-flip-vertical { 19 | filter: none; 20 | } 21 | -------------------------------------------------------------------------------- /statics/font-awesome-4.7.0/less/path.less: -------------------------------------------------------------------------------- 1 | /* FONT PATH 2 | * -------------------------- */ 3 | 4 | @font-face { 5 | font-family: 'FontAwesome'; 6 | src: url('@{fa-font-path}/fontawesome-webfont.eot?v=@{fa-version}'); 7 | src: url('@{fa-font-path}/fontawesome-webfont.eot?#iefix&v=@{fa-version}') format('embedded-opentype'), 8 | url('@{fa-font-path}/fontawesome-webfont.woff2?v=@{fa-version}') format('woff2'), 9 | url('@{fa-font-path}/fontawesome-webfont.woff?v=@{fa-version}') format('woff'), 10 | url('@{fa-font-path}/fontawesome-webfont.ttf?v=@{fa-version}') format('truetype'), 11 | url('@{fa-font-path}/fontawesome-webfont.svg?v=@{fa-version}#fontawesomeregular') format('svg'); 12 | // src: url('@{fa-font-path}/FontAwesome.otf') format('opentype'); // used when developing fonts 13 | font-weight: normal; 14 | font-style: normal; 15 | } 16 | -------------------------------------------------------------------------------- /statics/font-awesome-4.7.0/scss/_path.scss: -------------------------------------------------------------------------------- 1 | /* FONT PATH 2 | * -------------------------- */ 3 | 4 | @font-face { 5 | font-family: 'FontAwesome'; 6 | src: url('#{$fa-font-path}/fontawesome-webfont.eot?v=#{$fa-version}'); 7 | src: url('#{$fa-font-path}/fontawesome-webfont.eot?#iefix&v=#{$fa-version}') format('embedded-opentype'), 8 | url('#{$fa-font-path}/fontawesome-webfont.woff2?v=#{$fa-version}') format('woff2'), 9 | url('#{$fa-font-path}/fontawesome-webfont.woff?v=#{$fa-version}') format('woff'), 10 | url('#{$fa-font-path}/fontawesome-webfont.ttf?v=#{$fa-version}') format('truetype'), 11 | url('#{$fa-font-path}/fontawesome-webfont.svg?v=#{$fa-version}#fontawesomeregular') format('svg'); 12 | // src: url('#{$fa-font-path}/FontAwesome.otf') format('opentype'); // used when developing fonts 13 | font-weight: normal; 14 | font-style: normal; 15 | } 16 | -------------------------------------------------------------------------------- /statics/font-awesome-4.7.0/less/animated.less: -------------------------------------------------------------------------------- 1 | // Animated Icons 2 | // -------------------------- 3 | 4 | .@{fa-css-prefix}-spin { 5 | -webkit-animation: fa-spin 2s infinite linear; 6 | animation: fa-spin 2s infinite linear; 7 | } 8 | 9 | .@{fa-css-prefix}-pulse { 10 | -webkit-animation: fa-spin 1s infinite steps(8); 11 | animation: fa-spin 1s infinite steps(8); 12 | } 13 | 14 | @-webkit-keyframes fa-spin { 15 | 0% { 16 | -webkit-transform: rotate(0deg); 17 | transform: rotate(0deg); 18 | } 19 | 100% { 20 | -webkit-transform: rotate(359deg); 21 | transform: rotate(359deg); 22 | } 23 | } 24 | 25 | @keyframes fa-spin { 26 | 0% { 27 | -webkit-transform: rotate(0deg); 28 | transform: rotate(0deg); 29 | } 30 | 100% { 31 | -webkit-transform: rotate(359deg); 32 | transform: rotate(359deg); 33 | } 34 | } 35 | -------------------------------------------------------------------------------- /statics/font-awesome-4.7.0/scss/_animated.scss: -------------------------------------------------------------------------------- 1 | // Spinning Icons 2 | // -------------------------- 3 | 4 | .#{$fa-css-prefix}-spin { 5 | -webkit-animation: fa-spin 2s infinite linear; 6 | animation: fa-spin 2s infinite linear; 7 | } 8 | 9 | .#{$fa-css-prefix}-pulse { 10 | -webkit-animation: fa-spin 1s infinite steps(8); 11 | animation: fa-spin 1s infinite steps(8); 12 | } 13 | 14 | @-webkit-keyframes fa-spin { 15 | 0% { 16 | -webkit-transform: rotate(0deg); 17 | transform: rotate(0deg); 18 | } 19 | 100% { 20 | -webkit-transform: rotate(359deg); 21 | transform: rotate(359deg); 22 | } 23 | } 24 | 25 | @keyframes fa-spin { 26 | 0% { 27 | -webkit-transform: rotate(0deg); 28 | transform: rotate(0deg); 29 | } 30 | 100% { 31 | -webkit-transform: rotate(359deg); 32 | transform: rotate(359deg); 33 | } 34 | } 35 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # CRISPR-BETS Desktop version 2 | 3 | * CRISPR-BETS (CRISPR-Base Editing To Stop codon) is developed for designing gRNA to knockout gene by CRISPR base editing system. 4 | 5 | * CRISPR-BETS is implemented with both web (http://bioinfor.yzu.edu.cn/crisprbets/) and desktop version, which are integrated into a user-friendly graphic user interface (GUI) and compatible with major operating systems (Win, MacOS, Linux). 6 | 7 | 8 | 9 | ### [Documentation](https://crispr-bets-online.readthedocs.io/en/latest/) 10 | 11 | [![Documentation Status](https://readthedocs.org/projects/crispr-bets-online/badge/?version=latest)](https://crispr-bets-online.readthedocs.io/en/latest/?badge=latest) 12 | 13 | ### Video tutorials 14 | 15 | [YouTube (EN)](https://www.youtube.com/watch?v=i8cZowJZ--s) 16 | 17 | [bilibili (中文)](https://www.bilibili.com/video/BV1c44y1z7TG) 18 | 19 | 20 | ![image](./statics/img/1.png) 21 | 22 | ![image](./statics/img/2.png) 23 | -------------------------------------------------------------------------------- /exonerate/exonerate_macos/info/recipe/meta.yaml.template: -------------------------------------------------------------------------------- 1 | {% set version = "2.4.0" %} 2 | 3 | package: 4 | name: exonerate 5 | version: {{ version }} 6 | 7 | source: 8 | url: http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/exonerate-{{ version }}.tar.gz 9 | sha256: f849261dc7c97ef1f15f222e955b0d3daf994ec13c9db7766f1ac7e77baa4042 10 | 11 | build: 12 | number: 3 13 | 14 | requirements: 15 | build: 16 | - {{ compiler('c') }} 17 | - pkg-config 18 | - automake 19 | - autoconf 20 | host: 21 | - glib 22 | - pcre 23 | 24 | run: 25 | - glib 26 | - pcre 27 | 28 | test: 29 | commands: 30 | - 'exonerate 2>&1 | grep "exonerate: A generic sequence comparison tool"' 31 | 32 | about: 33 | home: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate 34 | license: GPL-3.0 35 | summary: Exonerate - A generic tool for pairwise sequence comparison / alignment 36 | 37 | extra: 38 | identifiers: 39 | - biotools:exonerate 40 | 41 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2021 yuechaowu 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /package.json: -------------------------------------------------------------------------------- 1 | { 2 | "name": "CRISPR-BETS", 3 | "version": "1.0.1", 4 | "main": "server.js", 5 | "dependencies": { 6 | "bio-parsers": "^5.5.5", 7 | "electron-squirrel-startup": "^1.0.0", 8 | "jquery": "^3.4.0", 9 | "jsonfile": "^5.0.0", 10 | "sync-exec": "^0.6.2", 11 | "ve-range-utils": "^2.5.3", 12 | "ve-sequence-utils": "^3.3.36", 13 | "wget-improved": "^3.0.2" 14 | }, 15 | "devDependencies": { 16 | "@electron-forge/cli": "^6.0.0-beta.54", 17 | "@electron-forge/maker-deb": "^6.0.0-beta.54", 18 | "@electron-forge/maker-rpm": "^6.0.0-beta.54", 19 | "@electron-forge/maker-squirrel": "^6.0.0-beta.54", 20 | "@electron-forge/maker-zip": "^6.0.0-beta.54", 21 | "electron": "^4.1.4" 22 | }, 23 | "scripts": { 24 | "start": "electron-forge start", 25 | "package": "electron-forge package", 26 | "make": "electron-forge make" 27 | }, 28 | "config": { 29 | "forge": { 30 | "packagerConfig": {}, 31 | "makers": [ 32 | { 33 | "name": "@electron-forge/maker-squirrel", 34 | "config": { 35 | "name": "CRISPR-BETS" 36 | } 37 | }, 38 | { 39 | "name": "@electron-forge/maker-zip", 40 | "platforms": [ 41 | "darwin" 42 | ] 43 | }, 44 | { 45 | "name": "@electron-forge/maker-deb", 46 | "config": {} 47 | }, 48 | { 49 | "name": "@electron-forge/maker-rpm", 50 | "config": {} 51 | } 52 | ] 53 | } 54 | } 55 | } 56 | -------------------------------------------------------------------------------- /cds.fa: -------------------------------------------------------------------------------- 1 | >cds 2 | ATGTCGGCTCTCACCACGTCCCAGCTCGCCACCTCGGCCACCGGCTTCGGCATCGCCGACAGGTCGGCGCCGTCGTCGCTGCTCCGCCACGGGTTCCAGGGCCTCAAGCCCCGCAGCCCCGCCGGCGGCGACGCGACGTCGCTCAGCGTGACGACCAGCGCGCGCGCGACGCCCAAGCAGCAGCGGTCGGTGCAGCGTGGCAGCCGGAGGTTCCCCTCCGTCGTCGTGTACGCCACCGGCGCCGGCATGAACGTCGTGTTCGTCGGCGCCGAGATGGCCCCCTGGAGCAAGACCGGCGGCCTCGGTGACGTCCTCGGTGGCCTCCCCCCTGCCATGGCTGCGAATGGCCACAGGGTCATGGTGATCTCTCCTCGGTACGACCAGTACAAGGACGCTTGGGATACCAGCGTTGTGGCTGAGATCAAGGTTGCAGACAGGTACGAGAGGGTGAGGTTTTTCCATTGCTACAAGCGTGGAGTCGACCGTGTGTTCATCGACCATCCGTCATTCCTGGAGAAGGTTTGGGGAAAGACCGGTGAGAAGATCTACGGACCTGACACTGGAGTTGATTACAAAGACAACCAGATGCGTTTCAGCCTTCTTTGCCAGGCAGCACTCGAGGCTCCTAGGATCCTAAACCTCAACAACAACCCATACTTCAAAGGAACTTATGGTGAGGATGTTGTGTTCGTCTGCAACGACTGGCACACTGGCCCACTGGCGAGCTACCTGAAGAACAACTACCAGCCCAATGGCATCTACAGGAATGCAAAGGTTGCTTTCTGCATCCACAACATCTCCTACCAGGGCCGTTTCGCTTTCGAGGATTACCCTGAGCTGAACCTCTCCGAGAGGTTCAGGTCATCCTTCGATTTCATCGACGGGTATGACACGCCGGTGGAGGGCAGGAAGATCAACTGGATGAAGGCCGGAATCCTGGAAGCCGACAGGGTGCTCACCGTGAGCCCGTACTACGCCGAGGAGCTCATCTCCGGCATCGCCAGGGGATGCGAGCTCGACAACATCATGCGGCTCACCGGCATCACCGGCATCGTCAACGGCATGGACGTCAGCGAGTGGGATCCTAGCAAGGACAAGTACATCACCGCCAAGTACGACGCAACCACGGCAATCGAGGCGAAGGCGCTGAACAAGGAGGCGTTGCAGGCGGAGGCGGGTCTTCCGGTCGACAGGAAAATCCCACTGATCGCGTTCATCGGCAGGCTGGAGGAACAGAAGGGCCCTGACGTCATGGCCGCCGCCATCCCGGAGCTCATGCAGGAGGACGTCCAGATCGTTCTTCTGGGTACTGGAAAGAAGAAGTTCGAGAAGCTGCTCAAGAGCATGGAGGAGAAGTATCCGGGCAAGGTGAGGGCCGTGGTGAAGTTCAACGCGCCGCTTGCTCATCTCATCATGGCCGGAGCCGACGTGCTCGCCGTCCCCAGCCGCTTCGAGCCCTGTGGACTCATCCAGCTGCAGGGGATGAGATACGGAACGCCCTGTGCTTGCGCGTCCACCGGTGGGCTCGTGGACACGGTCATCGAAGGCAAGACTGGTTTCCACATGGGCCGTCTCAGCGTCGACTGCAAGGTGGTGGAGCCAAGCGACGTGAAGAAGGTGGCGGCCACCCTGAAGCGCGCCATCAAGGTCGTCGGCACGCCGGCGTACGAGGAGATGGTCAGGAACTGCATGAACCAGGACCTCTCCTGGAAGGGGCCTGCGAAGAACTGGGAGAATGTGCTCCTGGGCCTGGGCGTCGCCGGCAGCGCGCCGGGGATCGAAGGCGACGAGATCGCGCCGCTCGCCAAGGAGAACGTGGCTGCTCCTTGA -------------------------------------------------------------------------------- /statics/font-awesome-4.7.0/less/mixins.less: -------------------------------------------------------------------------------- 1 | // Mixins 2 | // -------------------------- 3 | 4 | .fa-icon() { 5 | display: inline-block; 6 | font: normal normal normal @fa-font-size-base/@fa-line-height-base FontAwesome; // shortening font declaration 7 | font-size: inherit; // can't have font-size inherit on line above, so need to override 8 | text-rendering: auto; // optimizelegibility throws things off #1094 9 | -webkit-font-smoothing: antialiased; 10 | -moz-osx-font-smoothing: grayscale; 11 | 12 | } 13 | 14 | .fa-icon-rotate(@degrees, @rotation) { 15 | -ms-filter: "progid:DXImageTransform.Microsoft.BasicImage(rotation=@{rotation})"; 16 | -webkit-transform: rotate(@degrees); 17 | -ms-transform: rotate(@degrees); 18 | transform: rotate(@degrees); 19 | } 20 | 21 | .fa-icon-flip(@horiz, @vert, @rotation) { 22 | -ms-filter: "progid:DXImageTransform.Microsoft.BasicImage(rotation=@{rotation}, mirror=1)"; 23 | -webkit-transform: scale(@horiz, @vert); 24 | -ms-transform: scale(@horiz, @vert); 25 | transform: scale(@horiz, @vert); 26 | } 27 | 28 | 29 | // Only display content to screen readers. A la Bootstrap 4. 30 | // 31 | // See: http://a11yproject.com/posts/how-to-hide-content/ 32 | 33 | .sr-only() { 34 | position: absolute; 35 | width: 1px; 36 | height: 1px; 37 | padding: 0; 38 | margin: -1px; 39 | overflow: hidden; 40 | clip: rect(0,0,0,0); 41 | border: 0; 42 | } 43 | 44 | // Use in conjunction with .sr-only to only display content when it's focused. 45 | // 46 | // Useful for "Skip to main content" links; see http://www.w3.org/TR/2013/NOTE-WCAG20-TECHS-20130905/G1 47 | // 48 | // Credit: HTML5 Boilerplate 49 | 50 | .sr-only-focusable() { 51 | &:active, 52 | &:focus { 53 | position: static; 54 | width: auto; 55 | height: auto; 56 | margin: 0; 57 | overflow: visible; 58 | clip: auto; 59 | } 60 | } 61 | -------------------------------------------------------------------------------- /statics/font-awesome-4.7.0/scss/_mixins.scss: -------------------------------------------------------------------------------- 1 | // Mixins 2 | // -------------------------- 3 | 4 | @mixin fa-icon() { 5 | display: inline-block; 6 | font: normal normal normal #{$fa-font-size-base}/#{$fa-line-height-base} FontAwesome; // shortening font declaration 7 | font-size: inherit; // can't have font-size inherit on line above, so need to override 8 | text-rendering: auto; // optimizelegibility throws things off #1094 9 | -webkit-font-smoothing: antialiased; 10 | -moz-osx-font-smoothing: grayscale; 11 | 12 | } 13 | 14 | @mixin fa-icon-rotate($degrees, $rotation) { 15 | -ms-filter: "progid:DXImageTransform.Microsoft.BasicImage(rotation=#{$rotation})"; 16 | -webkit-transform: rotate($degrees); 17 | -ms-transform: rotate($degrees); 18 | transform: rotate($degrees); 19 | } 20 | 21 | @mixin fa-icon-flip($horiz, $vert, $rotation) { 22 | -ms-filter: "progid:DXImageTransform.Microsoft.BasicImage(rotation=#{$rotation}, mirror=1)"; 23 | -webkit-transform: scale($horiz, $vert); 24 | -ms-transform: scale($horiz, $vert); 25 | transform: scale($horiz, $vert); 26 | } 27 | 28 | 29 | // Only display content to screen readers. A la Bootstrap 4. 30 | // 31 | // See: http://a11yproject.com/posts/how-to-hide-content/ 32 | 33 | @mixin sr-only { 34 | position: absolute; 35 | width: 1px; 36 | height: 1px; 37 | padding: 0; 38 | margin: -1px; 39 | overflow: hidden; 40 | clip: rect(0,0,0,0); 41 | border: 0; 42 | } 43 | 44 | // Use in conjunction with .sr-only to only display content when it's focused. 45 | // 46 | // Useful for "Skip to main content" links; see http://www.w3.org/TR/2013/NOTE-WCAG20-TECHS-20130905/G1 47 | // 48 | // Credit: HTML5 Boilerplate 49 | 50 | @mixin sr-only-focusable { 51 | &:active, 52 | &:focus { 53 | position: static; 54 | width: auto; 55 | height: auto; 56 | margin: 0; 57 | overflow: visible; 58 | clip: auto; 59 | } 60 | } 61 | -------------------------------------------------------------------------------- /exonerate/exonerate_linux/share/man/man1/fastautils.1: -------------------------------------------------------------------------------- 1 | .\" iPCRess man Page 2 | .TH fastautils 1 "March 2003" fastautils "FASTA format file manipulation utilities" 3 | .SH NAME 4 | .\" 5 | fastautils \- FASTA format file manipulation utilities 6 | 7 | .SH SYNOPSIS 8 | 9 | .B fastachecksum [ options ] 10 | .P 11 | .B fastaclean 12 | .P 13 | .B fastaclip 14 | .P 15 | .B fastacomposition 16 | .P 17 | .B fastadiff 18 | .P 19 | .B fastaexplode 20 | .P 21 | .B fastafetch 22 | .P 23 | .B fastahardmask 24 | .P 25 | .B fastaindex 26 | .P 27 | .B fastalength 28 | .P 29 | .B fastanrdb 30 | .P 31 | .B fastaoverlap 32 | .P 33 | .B fastareformat 34 | .P 35 | .B fastaremove 36 | .P 37 | .B fastarevcomp 38 | .P 39 | .B fastasoftmask 40 | .P 41 | .B fastasort 42 | .P 43 | .B fastasplit 44 | .P 45 | .B fastasubseq 46 | .P 47 | .B fastatranslate 48 | .P 49 | .B fastavalidcds 50 | .P 51 | .\" 52 | 53 | .SH DESCRIPTION 54 | These are utilities for the manipulation of FASTA format sequence 55 | databases which are distributed with the exonerate sequence alignment 56 | program. 57 | .P 58 | .\" 59 | ... 60 | .\" 61 | .RE 62 | .\" 63 | .SH ENVIRONMENT 64 | Not documented yet. 65 | .\" 66 | .SH EXAMPLES 67 | .\" 68 | .B "fastalength sequence.fasta" 69 | .RS 70 | blah blah 71 | .RE 72 | .\" 73 | .SH VERSION 74 | This documentation accompanies version 2.2.0 of the exonerate package. 75 | .\" 76 | .SH AUTHOR 77 | Guy St.C. Slater. . 78 | .L 79 | See the AUTHORS file accompanying the source code 80 | for a list of contributors. 81 | .SH AVAILABILITY 82 | This source code for the exonerate package is available 83 | under the terms of the GNU 84 | .I general 85 | public licence. 86 | 87 | Please see the file COPYING which was distrubuted with this package, 88 | or http://www.gnu.org/licenses/gpl.txt for details. 89 | 90 | This package has been developed as part of the ensembl project. 91 | Please see http://www.ensembl.org/ for more information. 92 | .SH "SEE ALSO" 93 | .BR exonerate (1), e-PCR 94 | -------------------------------------------------------------------------------- /exonerate/exonerate_macos/share/man/man1/fastautils.1: -------------------------------------------------------------------------------- 1 | .\" iPCRess man Page 2 | .TH fastautils 1 "March 2003" fastautils "FASTA format file manipulation utilities" 3 | .SH NAME 4 | .\" 5 | fastautils \- FASTA format file manipulation utilities 6 | 7 | .SH SYNOPSIS 8 | 9 | .B fastachecksum [ options ] 10 | .P 11 | .B fastaclean 12 | .P 13 | .B fastaclip 14 | .P 15 | .B fastacomposition 16 | .P 17 | .B fastadiff 18 | .P 19 | .B fastaexplode 20 | .P 21 | .B fastafetch 22 | .P 23 | .B fastahardmask 24 | .P 25 | .B fastaindex 26 | .P 27 | .B fastalength 28 | .P 29 | .B fastanrdb 30 | .P 31 | .B fastaoverlap 32 | .P 33 | .B fastareformat 34 | .P 35 | .B fastaremove 36 | .P 37 | .B fastarevcomp 38 | .P 39 | .B fastasoftmask 40 | .P 41 | .B fastasort 42 | .P 43 | .B fastasplit 44 | .P 45 | .B fastasubseq 46 | .P 47 | .B fastatranslate 48 | .P 49 | .B fastavalidcds 50 | .P 51 | .\" 52 | 53 | .SH DESCRIPTION 54 | These are utilities for the manipulation of FASTA format sequence 55 | databases which are distributed with the exonerate sequence alignment 56 | program. 57 | .P 58 | .\" 59 | ... 60 | .\" 61 | .RE 62 | .\" 63 | .SH ENVIRONMENT 64 | Not documented yet. 65 | .\" 66 | .SH EXAMPLES 67 | .\" 68 | .B "fastalength sequence.fasta" 69 | .RS 70 | blah blah 71 | .RE 72 | .\" 73 | .SH VERSION 74 | This documentation accompanies version 2.2.0 of the exonerate package. 75 | .\" 76 | .SH AUTHOR 77 | Guy St.C. Slater. . 78 | .L 79 | See the AUTHORS file accompanying the source code 80 | for a list of contributors. 81 | .SH AVAILABILITY 82 | This source code for the exonerate package is available 83 | under the terms of the GNU 84 | .I general 85 | public licence. 86 | 87 | Please see the file COPYING which was distrubuted with this package, 88 | or http://www.gnu.org/licenses/gpl.txt for details. 89 | 90 | This package has been developed as part of the ensembl project. 91 | Please see http://www.ensembl.org/ for more information. 92 | .SH "SEE ALSO" 93 | .BR exonerate (1), e-PCR 94 | -------------------------------------------------------------------------------- /exonerate/exonerate_macos/info/recipe/meta.yaml: -------------------------------------------------------------------------------- 1 | # This file created by conda-build 3.18.9 2 | # meta.yaml template originally from: 3 | # /Users/runner/runners/2.159.2/work/bioconda-recipes/bioconda-recipes/recipes/exonerate, last modified Tue Oct 29 09:23:37 2019 4 | # ------------------------------------------------ 5 | 6 | package: 7 | name: exonerate 8 | version: 2.4.0 9 | source: 10 | sha256: f849261dc7c97ef1f15f222e955b0d3daf994ec13c9db7766f1ac7e77baa4042 11 | url: http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/exonerate-2.4.0.tar.gz 12 | build: 13 | number: '3' 14 | string: hbe7ca29_3 15 | requirements: 16 | build: 17 | - autoconf 2.69 pl526h1de35cc_9 18 | - automake 1.16.1 pl526_1003 19 | - cctools 895 h7512d6f_0 20 | - clang 4.0.1 h662ec87_0 21 | - clang_osx-64 4.0.1 h1ce6c1d_17 22 | - compiler-rt 4.0.1 h5487866_0 23 | - ld64 274.2 h7c2db76_0 24 | - libcxx 4.0.1 h579ed51_0 25 | - libcxxabi 4.0.1 hebd6815_0 26 | - libiconv 1.15 h01d97ff_1005 27 | - llvm 4.0.1 hc748206_0 28 | - llvm-lto-tapi 4.0.1 h6701bc3_0 29 | - m4 1.4.18 h1de35cc_1001 30 | - perl 5.26.2 haec8ef5_1006 31 | - pkg-config 0.29.2 h112b980_1005 32 | host: 33 | - gettext 0.19.8.1 h46ab8bc_1002 34 | - glib 2.58.3 h9d45998_1002 35 | - libcxx 9.0.0 h89e68fa_1 36 | - libffi 3.2.1 h6de7cb9_1006 37 | - libiconv 1.15 h01d97ff_1005 38 | - pcre 8.43 h4a8c4bd_0 39 | - zlib 1.2.11 h0b31af3_1006 40 | run: 41 | - glib >=2.58.3,<3.0a0 42 | - pcre >=8.43,<9.0a0 43 | test: 44 | commands: 45 | - 'exonerate 2>&1 | grep "exonerate: A generic sequence comparison tool"' 46 | about: 47 | home: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate 48 | license: GPL-3.0 49 | summary: Exonerate - A generic tool for pairwise sequence comparison / alignment 50 | extra: 51 | copy_test_source_files: true 52 | final: true 53 | identifiers: 54 | - biotools:exonerate 55 | -------------------------------------------------------------------------------- /codon_info.json: -------------------------------------------------------------------------------- 1 | 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2 | -------------------------------------------------------------------------------- /dna.fa: -------------------------------------------------------------------------------- 1 | >dna 2 | GTAAAATGTGTTGCGGGAGGGAGAGGGGGAGAGAGAGATCGCGCGGGCTTCACGCAACGGCGCTACAAATAGCCACCCACACCACCACCCCCTCTCTCACCATTCCTTCAGTTCTTTGTCTATCTCAAGACACAAATAACTGCAGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGCTTCACTTCTCTGCTTGTGTTGTTCTGTTGTTCATCAGGAAGAACATCTGCAAGTTATACATATATGTTTATAATTCTTTGTTTCCCCTCTTATTCAGATCGATCACATGCATCTTTCATTGCTCGTTTTTCCTTACAAGTAGTCTCATACATGCTAATTTCTGTAAGGTGTTGGGCTGGAAATTAATTAATTAATTAATTGACTTGCCAAGATCCATATATATGTCCTGATATTAAATCTTCGTTCGTTATGTTTGGTTAGGCTGATCAATGTTATTCTAGAGTCTAGAGAAACACACCCAGGGGTTTTCCAACTAGCTCCACAAGATGGTGGGCTAGCTGACCTAGATTTGAAGTCTCACTCCTTATAATTATTTTATATTAGATCATTTTCTAATATTCGTGTCTTTTTTTATTCTAGAGTCTAGATCTTGTGTTCAACTCTCGTTAAATCATGTCTCTCGCCACTGGAGAAACAGATCAGGAGGGTTTATTTTGGGTATAGGTCAAAGCTAAGATTGAAATTCACAAATAGTAAAATCAGAATCCAACCAATTTTAGTAGCCGAGTTGGTCAAAGGAAAATGTATATAGCTAGATTTATTGTTTTGGCAAAAAAAAATCTGAATATGCAAAATACTTGTATATCTTTGTATTAAGAAGATGAAAATAAGTAGCAGAAAATTAAAAAATGGATTATATTTCCTGGGCTAAAAGAATTGTTGATTTGGCACAATTAAATTCAGTGTCAAGGTTTTGTGCAAGAATTCAGTGTGAAGGAATAGATTCTCTTCAAAACAATTTAATCATTCATCTGATCTGCTCAAAGCTCTGTGCATCTCCGGGTGCAACGGCCAGGATATTTATTGTGCAGTAAAAAAATGTCATATCCCCTAGCCACCCAAGAAACTGCTCCTTAAGTCCTTATAAGCACATATGGCATTGTAATATATATGTTTGAGTTTTAGCGACAATTTTTTTAAAAACTTTTGGTCCTTTTTATGAACGTTTTAAGTTTCACTGTCTTTTTTTTTCGAATTTTAAATGTAGCTTCAAATTCTAATCCCCAATCCAAATTGTAATAAACTTCAATTCTCCTAATTAACATCTTAATTCATTTATTTGAAAACCAGTTCAAATTCTTTTAGGCTCACCAAACCTTAAACAATTCAATTCAGTGCAGAGATCTTCCACAGCAACAGCTAGACAACCACCATGTCGGCTCTCACCACGTCCCAGCTCGCCACCTCGGCCACCGGCTTCGGCATCGCCGACAGGTCGGCGCCGTCGTCGCTGCTCCGCCACGGGTTCCAGGGCCTCAAGCCCCGCAGCCCCGCCGGCGGCGACGCGACGTCGCTCAGCGTGACGACCAGCGCGCGCGCGACGCCCAAGCAGCAGCGGTCGGTGCAGCGTGGCAGCCGGAGGTTCCCCTCCGTCGTCGTGTACGCCACCGGCGCCGGCATGAACGTCGTGTTCGTCGGCGCCGAGATGGCCCCCTGGAGCAAGACCGGCGGCCTCGGTGACGTCCTCGGTGGCCTCCCCCCTGCCATGGCTGTAAGCACACACAAACTTCGATCGCTCGTCGTCGCTGACCGTCGTCGTCTTCAACTGTTCTTGATCATCGCATTGGATGGATGTGTAATGTTGTGTTCTTGTGTTCTTTGCAGGCGAATGGCCACAGGGTCATGGTGATCTCTCCTCGGTACGACCAGTACAAGGACGCTTGGGATACCAGCGTTGTGGCTGAGGTAGGAGCATATGCGTGATCAGATCATCACAAGATCGATTAGCTTTAGATGATTTGTTACATTTCGCAAGATTTTAACCCAAGTTTTTGTGGTGCAATTCATTGCAGATCAAGGTTGCAGACAGGTACGAGAGGGTGAGGTTTTTCCATTGCTACAAGCGTGGAGTCGACCGTGTGTTCATCGACCATCCGTCATTCCTGGAGAAGGTGGAGTCATCATTAGTTTACCTTTTTTGTTTTTACTGAATTATTAACAGTGCATTTAGCAGTTGGACTGAGCTTAGCTTCCACTGGTGATTTCAGGTTTGGGGAAAGACCGGTGAGAAGATCTACGGACCTGACACTGGAGTTGATTACAAAGACAACCAGATGCGTTTCAGCCTTCTTTGCCAGGTCAGTGATTACTTCTATCTGATGATGGTTGGAAGCATCACGAGTTTACCATAGTATGTATGGATTCATAACTAATTCGTGTATTGATGCTACCTGCAGGCAGCACTCGAGGCTCCTAGGATCCTAAACCTCAACAACAACCCATACTTCAAAGGAACTTATGGTGAGTTACAATTGATCTCAAGATCTTATAACTTTCTTCGAAGGAATCCATGATGATCAGACTAATTCCTTCCGGTTTGTTACTGACAACAGGTGAGGATGTTGTGTTCGTCTGCAACGACTGGCACACTGGCCCACTGGCGAGCTACCTGAAGAACAACTACCAGCCCAATGGCATCTACAGGAATGCAAAGGTCTATGCTTGTTCTTGCCATACCAACTCAAATCTGCATGCACACTGCATTCTGTTCAGAAACTGACTGTCTGAATCTTTTTCACTGCAGGTTGCTTTCTGCATCCACAACATCTCCTACCAGGGCCGTTTCGCTTTCGAGGATTACCCTGAGCTGAACCTCTCCGAGAGGTTCAGGTCATCCTTCGATTTCATCGACGGGTATGAGTAAGATTCTAAGAGTAACTTACTGTCAATTCGCCATATATCGATTCAATCCAAGATCCTTTTGAGCTGACAACCCTGCACTACTGTCCATCGTTCAAATCCGGTTAAATTTCAGGTATGACACGCCGGTGGAGGGCAGGAAGATCAACTGGATGAAGGCCGGAATCCTGGAAGCCGACAGGGTGCTCACCGTGAGCCCGTACTACGCCGAGGAGCTCATCTCCGGCATCGCCAGGGGATGCGAGCTCGACAACATCATGCGGCTCACCGGCATCACCGGCATCGTCAACGGCATGGACGTCAGCGAGTGGGATCCTAGCAAGGACAAGTACATCACCGCCAAGTACGACGCAACCACGGTAAGAACGAATGCATTCTTCACAAGATATGCAATCTGAATTTTCTTTGAAAAAGAAATTATCATCTGTCACTTCTTGATTGATTCTGACAAGGCAAGAATGAGTGACAAATTTCAGGCAATCGAGGCGAAGGCGCTGAACAAGGAGGCGTTGCAGGCGGAGGCGGGTCTTCCGGTCGACAGGAAAATCCCACTGATCGCGTTCATCGGCAGGCTGGAGGAACAGAAGGGCCCTGACGTCATGGCCGCCGCCATCCCGGAGCTCATGCAGGAGGACGTCCAGATCGTTCTTCTGGTATAATATAATACACTACAAGACACACTTGCACGATATGCCAAAAATTCAGAACAAATTCAGTGGCAAAAAAAAAACTCGAATATTAGGGAAGGACCTAATAATATCAAATAATTAGAAGGGGTGAGGCTTTGAACCCAGATCGTCTAGTCCACCACCTTGTGGAGTTAGCCGGAAGACCTCTGAGCATTTCTCAATTCAGTGGCAAATGATGTGTATAATTTTGATCCGTGTGTGTTTCAGGGTACTGGAAAGAAGAAGTTCGAGAAGCTGCTCAAGAGCATGGAGGAGAAGTATCCGGGCAAGGTGAGGGCCGTGGTGAAGTTCAACGCGCCGCTTGCTCATCTCATCATGGCCGGAGCCGACGTGCTCGCCGTCCCCAGCCGCTTCGAGCCCTGTGGACTCATCCAGCTGCAGGGGATGAGATACGGAACGGTATACAATTTCCATCTATCAATTCGATTGTTCGATTTCATCTTTGTGCAATGCAATGCAATTGCAAATGCAAATGCATGATGATTTTCCTTGTTGATTTCTCCAGCCCTGTGCTTGCGCGTCCACCGGTGGGCTCGTGGACACGGTCATCGAAGGCAAGACTGGTTTCCACATGGGCCGTCTCAGCGTCGACGTAAGCCTATACATTTACATAACAATCAGATATGACACATCCTAATACCGATAAGTCGGTACACTACTACACATTTACATGGTTGCTGGTTATATGGTTTTTTTGGCAGTGCAAGGTGGTGGAGCCAAGCGACGTGAAGAAGGTGGCGGCCACCCTGAAGCGCGCCATCAAGGTCGTCGGCACGCCGGCGTACGAGGAGATGGTCAGGAACTGCATGAACCAGGACCTCTCCTGGAAGGTATAAATTACGAAACAAATTTAACCCAAACATATACTATATACTCCCTCCGCTTCTAAATATTCAACGCCGTTGTCTTTTTTAAATATGTTTGACCATTCGTCTTATTAAAAAAATTAAATAATTATAAATTCTTTTCCTATCATTTGATTCATTGTTAAATATACTTATATGTATACATATAGTTTTACATATTTCATAAAATTTTTTGAACAAGACGAACGGTCAAACATGTGCTAAAAAGTTAACGGTGTCGAATATTCAGAAACGGAGGGAGTATAAACGTCTTGTTCAGAAGTTCAGAGATTCACCTGTCTGATGCTGATGATGATTAATTGTTTGCAACATGGATTTCAGGGGCCTGCGAAGAACTGGGAGAATGTGCTCCTGGGCCTGGGCGTCGCCGGCAGCGCGCCGGGGATCGAAGGCGACGAGATCGCGCCGCTCGCCAAGGAGAACGTGGCTGCTCCTTGAAGAGCCTGAGATCTACATATGGAGTGATTAATTAATATAGCAGTATATGGATGAGAGACGAATGAACCAGTGGTTTGTTTGTTGTAGTGAATTTGTAGCTATAGCCAATTATATAGGCTAATAAGTTTGATGTTGTACTCTTCTGGGTGTGCTTAAGTATCTTATCGGACCCTGAATTTATGTGTGTGGCTTATTGCCAATAATATTAAGTAATAAAGGGTTTATTATATTATTATATATGTTA -------------------------------------------------------------------------------- /result.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | Result 6 | 7 | 8 | 9 | 10 | 11 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 48 | 49 | 50 | 51 |
52 | 53 | 54 |
55 |
56 | Location 57 |
58 | 59 | 60 |
61 | 62 |
63 |
64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 95 | 96 | 97 | 121 | 122 | 123 | 124 | 125 | 126 | 127 | -------------------------------------------------------------------------------- /exonerate/exonerate_macos/info/about.json: -------------------------------------------------------------------------------- 1 | { 2 | "channels": [ 3 | "defaults", 4 | "conda-forge", 5 | "bioconda", 6 | "defaults" 7 | ], 8 | "conda_build_version": "3.18.9", 9 | "conda_private": false, 10 | "conda_version": "4.6.14", 11 | "env_vars": { 12 | "CIO_TEST": "" 13 | }, 14 | "extra": { 15 | "copy_test_source_files": true, 16 | "final": true, 17 | "identifiers": [ 18 | "biotools:exonerate" 19 | ] 20 | }, 21 | "home": "https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate", 22 | "identifiers": [], 23 | "keywords": [], 24 | "license": "GPL-3.0", 25 | "root_pkgs": [ 26 | "ruamel_yaml 0.15.71 py36h1de35cc_1000", 27 | "libedit 3.1.20170329 hcfe32e1_1001", 28 | "numpy 1.17.3 py36hde6bac1_0", 29 | 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/Users/runner/miniconda/envs/bioconda/conda-bld/exonerate_1572343936206/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh binary bin/fastasort 23 | /Users/runner/miniconda/envs/bioconda/conda-bld/exonerate_1572343936206/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh binary bin/fastasplit 24 | /Users/runner/miniconda/envs/bioconda/conda-bld/exonerate_1572343936206/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh binary bin/fastasubseq 25 | /Users/runner/miniconda/envs/bioconda/conda-bld/exonerate_1572343936206/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh binary bin/fastatranslate 26 | /Users/runner/miniconda/envs/bioconda/conda-bld/exonerate_1572343936206/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh binary bin/fastavalidcds 27 | /Users/runner/miniconda/envs/bioconda/conda-bld/exonerate_1572343936206/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh binary bin/ipcress 28 | -------------------------------------------------------------------------------- /exonerate/exonerate_linux/share/man/man1/ipcress.1: -------------------------------------------------------------------------------- 1 | .\" iPCRess man Page 2 | .TH ipcress 1 "March 2003" ipcress "PCR simulation tool" 3 | .SH NAME 4 | .\" 5 | ipcress \- In-silico PCR experiment simulation system 6 | .SH SYNOPSIS 7 | .B ipcress [ options ] 8 | 9 | .SH DESCRIPTION 10 | .BR ipcress 11 | is the 12 | .IR I n-silico 13 | .IR PCR 14 | .IR E xperiment 15 | .IR S imulation 16 | .IR S ystem. 17 | 18 | This is a tool for simulation of PCR experiments. 19 | You supply a file containing primers and a set of sequences, 20 | and it predicts PCR products. 21 | .P 22 | .\" 23 | Ipcress is similar to the e-PCR program from the NCBI, 24 | but is much faster, and does not suffer from problems 25 | identifying matches when there are ambiguity symbols 26 | near primer ends. 27 | .P 28 | .\" 29 | If you supply many primers pairs together, 30 | ipcress will simulate the PCR experiments in parallel, 31 | allowing genome wide simulation of large numbers of experiments. 32 | It uses many libraries from the 33 | .B exonerate 34 | sequence comparison tool. 35 | .\" 36 | .RE 37 | .SH INPUT FORMAT 38 | .T 39 | The input for ipcress is a simple white-space delimited file 40 | describing one experiment per line. Each line contains 41 | the following 5 fields: 42 | .\" 43 | .PP 44 | .RS 45 | .PD 0 46 | .\" 47 | .TP 18 48 | .B id 49 | An identifier for this experiment 50 | .\" 51 | .TP 18 52 | .B primer_A 53 | Sequence for the first primer 54 | .\" 55 | .TP 18 56 | .B primer_B 57 | Sequence for the second primer 58 | .\" 59 | .TP 18 60 | .B min_product_len 61 | Minimum product length to report 62 | .\" 63 | .TP 18 64 | .B max_product_len 65 | Maximum product length to report 66 | .\" 67 | .PD 68 | .RE 69 | .P 70 | Here is an example line in this format: 71 | .SP 72 | .nf 73 | 74 | ID0001 CATGCATGCATGC CGATGCANGCATGCT 900 1100 75 | .SP 76 | .fi 77 | .\" 78 | .RE 79 | .SH OUTPUT FORMAT 80 | .T 81 | The output format describes one PCR product per-line, 82 | and is prefixed by "ipcress:", followed by the following 11 fields: 83 | .\" 84 | .PP 85 | .RS 86 | .PD 0 87 | .\" 88 | .TP 16 89 | .B sequence_id 90 | The sequence identifier 91 | .\" 92 | .TP 16 93 | .B experiment_id 94 | The PCR experiment id 95 | .\" 96 | .TP 16 97 | .B product_length 98 | The PCR product length 99 | .\" 100 | .TP 16 101 | .B primer_5 102 | The 5' primer (either A or B) 103 | .\" 104 | .TP 16 105 | .B pos_5 106 | Position of the 5' primer 107 | .\" 108 | .TP 16 109 | .B mismatch_5 110 | Number of mismatches on 5' primer 111 | .\" 112 | .TP 16 113 | .B primer_3 114 | | 115 | .\" 116 | .TP 16 117 | .B pos_3 118 | | Same fields for the 3' primer 119 | .\" 120 | .TP 16 121 | .B mismatch_3 122 | | 123 | .\" 124 | .TP 16 125 | .B description 126 | A description of the PCR product 127 | .\" 128 | .PD 129 | .RE 130 | .P 131 | .\" 132 | The description field is one of the following 4 strings: 133 | .\" 134 | .PP 135 | .RS 136 | .PD 0 137 | .\" 138 | .TP 10 139 | .B forward 140 | Normal product, primer A followed by B 141 | .\" 142 | .TP 10 143 | .B revcomp 144 | Normal product, primer B followed by A 145 | .\" 146 | .TP 10 147 | .B single_A 148 | Bad product generated by primer_A only 149 | .\" 150 | .TP 10 151 | .B single_B 152 | Bad product generated by primer_B only 153 | .\" 154 | .PD 155 | .RE 156 | .P 157 | .\" 158 | There is also a human-readable output displayed, 159 | is not designed for parsing (see: --pretty below). 160 | .\" 161 | .RE 162 | .SH GENERAL OPTIONS 163 | .T 164 | Most arguments have short and long forms. The long forms 165 | are more likely to be stable over time, and hence should 166 | be used in scripts which call ipcress. 167 | .\" 168 | .TP 169 | .B "\-h | \--shorthelp" 170 | Show help. 171 | This will display a concise summary of the available options, 172 | defaults and values currently set. 173 | .\" 174 | .TP 175 | .B "--help" 176 | This shows all the help options including the defaults, 177 | the value currently set, 178 | and the environment variable which may be used to set each parameter. 179 | There will be an indication of which options are mandatory. 180 | Mandatory options have no default, and must have a value supplied 181 | for ipcress to run. If mandatory options are used in order, 182 | their flags may be skipped from the command line (see examples below). 183 | Unlike this man page, the information from this option will always 184 | be up to date with the latest version of the program. 185 | .\" 186 | .TP 187 | .B "\-v | \--version" 188 | Display the version number. Also displays other information 189 | such as the build date and glib version used. 190 | .RE 191 | .\" 192 | .SH FILE INPUT OPTIONS 193 | .TP 194 | .B "-i | \--input " 195 | PCR experiment data in the ipcress file format described above. 196 | .TP 197 | .B "-s | \--sequence" 198 | Specify the sequences. 199 | Multiple files may be specified here, 200 | which reduces the FSM building overhead, and makes ipcress 201 | run faster than running the process separately. 202 | .RE 203 | .\" 204 | .SH IPCRESS PARAMETERS 205 | .TP 206 | .B "\-m | \--mismatch " 207 | Specify the number of mismatches allowed per primer. 208 | Allowing mismatches reduces the speed of the program 209 | as a large primer neighbourhood must be constructed, 210 | and fewer experiments can be fitted in memory prior 211 | to each scan of the sequence databases. 212 | .\" 213 | .TP 214 | .B "\-M | \--memory" 215 | Specify the amount of memory the program should use. 216 | The more memory made available ipcress, the faster 217 | it will run, as more PCR experiments can be conducted 218 | in each scan of the sequence databases. 219 | This does not include memory used during the scan 220 | (for storing partial results and sequences), so the 221 | actual amount of memory used will be slightly higher. 222 | .\" 223 | .TP 224 | .B "\-p | \--pretty" 225 | Display results in a human-readable format, not designed for parsing. 226 | .\" 227 | .TP 228 | .B "\-P | \--products" 229 | Display PCR products as a FASTA format sequence. 230 | .\" 231 | .TP 232 | .B "\-S | \--seed" 233 | Specifiy the seed length for the wordneighbourhood for the FSM. 234 | If set to zero, the full primer is used. 235 | Shorter words reduce the size of the neighbourhood, 236 | but increase the time taken by ipcress to filter 237 | false positive matches. 238 | .\" 239 | .SH ENVIRONMENT 240 | Not documented yet. 241 | .\" 242 | .SH EXAMPLES 243 | .\" 244 | .B "ipcress test.ipcress sequence.fasta" 245 | .RS 246 | This is the simplest way that ipcress can be used. 247 | .RE 248 | .\" 249 | .B "ipcress dbsts_human.ipcress --sequence ncbi30/*.fasta --mismatch 1" 250 | .RS 251 | Compare a input file against a set of fasta files, 252 | allowing one mismatch in each primer. 253 | .RE 254 | .\" 255 | .RE 256 | .SH VERSION 257 | This documentation accompanies version 2.2.0 of the exonerate package. 258 | .\" 259 | .SH AUTHOR 260 | Guy St.C. Slater. . 261 | .L 262 | See the AUTHORS file accompanying the source code 263 | for a list of contributors. 264 | .SH AVAILABILITY 265 | This source code for the exonerate package is available 266 | under the terms of the GNU 267 | .I general 268 | public licence. 269 | 270 | Please see the file COPYING which was distrubuted with this package, 271 | or http://www.gnu.org/licenses/gpl.txt for details. 272 | 273 | This package has been developed as part of the ensembl project. 274 | Please see http://www.ensembl.org/ for more information. 275 | .SH "SEE ALSO" 276 | .BR exonerate (1), e-PCR 277 | -------------------------------------------------------------------------------- /exonerate/exonerate_macos/share/man/man1/ipcress.1: -------------------------------------------------------------------------------- 1 | .\" iPCRess man Page 2 | .TH ipcress 1 "March 2003" ipcress "PCR simulation tool" 3 | .SH NAME 4 | .\" 5 | ipcress \- In-silico PCR experiment simulation system 6 | .SH SYNOPSIS 7 | .B ipcress [ options ] 8 | 9 | .SH DESCRIPTION 10 | .BR ipcress 11 | is the 12 | .IR I n-silico 13 | .IR PCR 14 | .IR E xperiment 15 | .IR S imulation 16 | .IR S ystem. 17 | 18 | This is a tool for simulation of PCR experiments. 19 | You supply a file containing primers and a set of sequences, 20 | and it predicts PCR products. 21 | .P 22 | .\" 23 | Ipcress is similar to the e-PCR program from the NCBI, 24 | but is much faster, and does not suffer from problems 25 | identifying matches when there are ambiguity symbols 26 | near primer ends. 27 | .P 28 | .\" 29 | If you supply many primers pairs together, 30 | ipcress will simulate the PCR experiments in parallel, 31 | allowing genome wide simulation of large numbers of experiments. 32 | It uses many libraries from the 33 | .B exonerate 34 | sequence comparison tool. 35 | .\" 36 | .RE 37 | .SH INPUT FORMAT 38 | .T 39 | The input for ipcress is a simple white-space delimited file 40 | describing one experiment per line. Each line contains 41 | the following 5 fields: 42 | .\" 43 | .PP 44 | .RS 45 | .PD 0 46 | .\" 47 | .TP 18 48 | .B id 49 | An identifier for this experiment 50 | .\" 51 | .TP 18 52 | .B primer_A 53 | Sequence for the first primer 54 | .\" 55 | .TP 18 56 | .B primer_B 57 | Sequence for the second primer 58 | .\" 59 | .TP 18 60 | .B min_product_len 61 | Minimum product length to report 62 | .\" 63 | .TP 18 64 | .B max_product_len 65 | Maximum product length to report 66 | .\" 67 | .PD 68 | .RE 69 | .P 70 | Here is an example line in this format: 71 | .SP 72 | .nf 73 | 74 | ID0001 CATGCATGCATGC CGATGCANGCATGCT 900 1100 75 | .SP 76 | .fi 77 | .\" 78 | .RE 79 | .SH OUTPUT FORMAT 80 | .T 81 | The output format describes one PCR product per-line, 82 | and is prefixed by "ipcress:", followed by the following 11 fields: 83 | .\" 84 | .PP 85 | .RS 86 | .PD 0 87 | .\" 88 | .TP 16 89 | .B sequence_id 90 | The sequence identifier 91 | .\" 92 | .TP 16 93 | .B experiment_id 94 | The PCR experiment id 95 | .\" 96 | .TP 16 97 | .B product_length 98 | The PCR product length 99 | .\" 100 | .TP 16 101 | .B primer_5 102 | The 5' primer (either A or B) 103 | .\" 104 | .TP 16 105 | .B pos_5 106 | Position of the 5' primer 107 | .\" 108 | .TP 16 109 | .B mismatch_5 110 | Number of mismatches on 5' primer 111 | .\" 112 | .TP 16 113 | .B primer_3 114 | | 115 | .\" 116 | .TP 16 117 | .B pos_3 118 | | Same fields for the 3' primer 119 | .\" 120 | .TP 16 121 | .B mismatch_3 122 | | 123 | .\" 124 | .TP 16 125 | .B description 126 | A description of the PCR product 127 | .\" 128 | .PD 129 | .RE 130 | .P 131 | .\" 132 | The description field is one of the following 4 strings: 133 | .\" 134 | .PP 135 | .RS 136 | .PD 0 137 | .\" 138 | .TP 10 139 | .B forward 140 | Normal product, primer A followed by B 141 | .\" 142 | .TP 10 143 | .B revcomp 144 | Normal product, primer B followed by A 145 | .\" 146 | .TP 10 147 | .B single_A 148 | Bad product generated by primer_A only 149 | .\" 150 | .TP 10 151 | .B single_B 152 | Bad product generated by primer_B only 153 | .\" 154 | .PD 155 | .RE 156 | .P 157 | .\" 158 | There is also a human-readable output displayed, 159 | is not designed for parsing (see: --pretty below). 160 | .\" 161 | .RE 162 | .SH GENERAL OPTIONS 163 | .T 164 | Most arguments have short and long forms. The long forms 165 | are more likely to be stable over time, and hence should 166 | be used in scripts which call ipcress. 167 | .\" 168 | .TP 169 | .B "\-h | \--shorthelp" 170 | Show help. 171 | This will display a concise summary of the available options, 172 | defaults and values currently set. 173 | .\" 174 | .TP 175 | .B "--help" 176 | This shows all the help options including the defaults, 177 | the value currently set, 178 | and the environment variable which may be used to set each parameter. 179 | There will be an indication of which options are mandatory. 180 | Mandatory options have no default, and must have a value supplied 181 | for ipcress to run. If mandatory options are used in order, 182 | their flags may be skipped from the command line (see examples below). 183 | Unlike this man page, the information from this option will always 184 | be up to date with the latest version of the program. 185 | .\" 186 | .TP 187 | .B "\-v | \--version" 188 | Display the version number. Also displays other information 189 | such as the build date and glib version used. 190 | .RE 191 | .\" 192 | .SH FILE INPUT OPTIONS 193 | .TP 194 | .B "-i | \--input " 195 | PCR experiment data in the ipcress file format described above. 196 | .TP 197 | .B "-s | \--sequence" 198 | Specify the sequences. 199 | Multiple files may be specified here, 200 | which reduces the FSM building overhead, and makes ipcress 201 | run faster than running the process separately. 202 | .RE 203 | .\" 204 | .SH IPCRESS PARAMETERS 205 | .TP 206 | .B "\-m | \--mismatch " 207 | Specify the number of mismatches allowed per primer. 208 | Allowing mismatches reduces the speed of the program 209 | as a large primer neighbourhood must be constructed, 210 | and fewer experiments can be fitted in memory prior 211 | to each scan of the sequence databases. 212 | .\" 213 | .TP 214 | .B "\-M | \--memory" 215 | Specify the amount of memory the program should use. 216 | The more memory made available ipcress, the faster 217 | it will run, as more PCR experiments can be conducted 218 | in each scan of the sequence databases. 219 | This does not include memory used during the scan 220 | (for storing partial results and sequences), so the 221 | actual amount of memory used will be slightly higher. 222 | .\" 223 | .TP 224 | .B "\-p | \--pretty" 225 | Display results in a human-readable format, not designed for parsing. 226 | .\" 227 | .TP 228 | .B "\-P | \--products" 229 | Display PCR products as a FASTA format sequence. 230 | .\" 231 | .TP 232 | .B "\-S | \--seed" 233 | Specifiy the seed length for the wordneighbourhood for the FSM. 234 | If set to zero, the full primer is used. 235 | Shorter words reduce the size of the neighbourhood, 236 | but increase the time taken by ipcress to filter 237 | false positive matches. 238 | .\" 239 | .SH ENVIRONMENT 240 | Not documented yet. 241 | .\" 242 | .SH EXAMPLES 243 | .\" 244 | .B "ipcress test.ipcress sequence.fasta" 245 | .RS 246 | This is the simplest way that ipcress can be used. 247 | .RE 248 | .\" 249 | .B "ipcress dbsts_human.ipcress --sequence ncbi30/*.fasta --mismatch 1" 250 | .RS 251 | Compare a input file against a set of fasta files, 252 | allowing one mismatch in each primer. 253 | .RE 254 | .\" 255 | .RE 256 | .SH VERSION 257 | This documentation accompanies version 2.2.0 of the exonerate package. 258 | .\" 259 | .SH AUTHOR 260 | Guy St.C. Slater. . 261 | .L 262 | See the AUTHORS file accompanying the source code 263 | for a list of contributors. 264 | .SH AVAILABILITY 265 | This source code for the exonerate package is available 266 | under the terms of the GNU 267 | .I general 268 | public licence. 269 | 270 | Please see the file COPYING which was distrubuted with this package, 271 | or http://www.gnu.org/licenses/gpl.txt for details. 272 | 273 | This package has been developed as part of the ensembl project. 274 | Please see http://www.ensembl.org/ for more information. 275 | .SH "SEE ALSO" 276 | .BR exonerate (1), e-PCR 277 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | # Created by .ignore support plugin (hsz.mobi) 2 | ### VisualStudioCode template 3 | .vscode/* 4 | !.vscode/settings.json 5 | !.vscode/tasks.json 6 | !.vscode/launch.json 7 | !.vscode/extensions.json 8 | ### Linux template 9 | *~ 10 | 11 | # 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-*- 553 | *~ 554 | \#*\# 555 | /.emacs.desktop 556 | /.emacs.desktop.lock 557 | *.elc 558 | auto-save-list 559 | tramp 560 | .\#* 561 | 562 | # Org-mode 563 | .org-id-locations 564 | *_archive 565 | 566 | # flymake-mode 567 | *_flymake.* 568 | 569 | # eshell files 570 | /eshell/history 571 | /eshell/lastdir 572 | 573 | # elpa packages 574 | /elpa/ 575 | 576 | # reftex files 577 | *.rel 578 | 579 | # AUCTeX auto folder 580 | /auto/ 581 | 582 | # cask packages 583 | .cask/ 584 | dist/ 585 | 586 | # Flycheck 587 | flycheck_*.el 588 | 589 | # server auth directory 590 | /server/ 591 | 592 | # projectiles files 593 | .projectile 594 | 595 | # directory configuration 596 | .dir-locals.el -------------------------------------------------------------------------------- /exonerate/exonerate_linux/share/man/man1/exonerate-server.1: -------------------------------------------------------------------------------- 1 | .\" Exonerate man Page 2 | .TH exonerate-server 1 "January 2008" exonerate-server "sequence comparison server" 3 | .SH NAME 4 | .\" 5 | exonerate-server \- a sequence comparison server for exonerate 6 | .\" 7 | 8 | .SH SYNOPSIS 9 | .B exonerate-server [ options ] 10 | .\" 11 | 12 | .SH DESCRIPTION 13 | .BR exonerate-server 14 | is a multi-threaded server for the exonerate sequence alignment program. 15 | 16 | It uses a set of sequences and a corresponding index file 17 | to allow fast of large datasets. 18 | .\" 19 | 20 | .RE 21 | .SH OVERVIEW 22 | .T 23 | .\" 24 | Firstly, an 25 | .B .esd 26 | file must be made from the sequence files. 27 | The 28 | .B .esd 29 | file is an Exonerate Sequence Dataset 30 | file, and can be used to group together any set 31 | of sequences where each sequences containing unique identifiers. 32 | This is done by using the 33 | .B fasta2esd 34 | utility. 35 | .RS 36 | .TP 37 | .B "fasta2esd genome.fasta genome.esd" 38 | .P 39 | .RE 40 | Next, an 41 | .B .esi 42 | file my be made from the 43 | .B .esd 44 | file. 45 | The 46 | .B .esi 47 | file is an Exonerate Sequence Index 48 | file, and contains an index or set of indices corresponding 49 | to a particular dataset. 50 | This is done by using the 51 | .B esd2esi 52 | utility. 53 | .\" 54 | .RS 55 | .TP 56 | .B "esd2esi genome.esd genome.esi" 57 | .P 58 | .RE 59 | Once the 60 | .B .esi 61 | file has been generated, the exonerate-server may be started. 62 | .RS 63 | .TP 64 | .B "exonerate-server genome.esi" 65 | .P 66 | .RE 67 | While the server is running, exonerate may be used to query 68 | the server by replacing the target sequences in the command line 69 | with the name of the server and port number. 70 | The default port number for the exonerate-server is 12886. 71 | .RS 72 | .TP 73 | .B "exonerate query.fasta localhost:12886" 74 | .P 75 | .RE 76 | 77 | .RE 78 | .SH OPTIONS 79 | .T 80 | Some of the command line options for the exonerate-server are the same as for the 81 | exonerate client, and these are documented in the man page for 82 | .B exonerate. 83 | The other options which are specific to 84 | .B exonerate-server 85 | are documented here. 86 | .TP 87 | .B "\--port" 88 | Specify the port on which the server should listen. 89 | By default, 90 | .B exonerate-server 91 | will listen on port 12886, but alternative ports may be specified with this 92 | option. 93 | .\" 94 | .TP 95 | .B "\--input" 96 | Specify the index file to be used when the server is started. 97 | This option is mandatory. The index file is a 98 | .B .esi 99 | file generated by the 100 | .B esd2esi 101 | utility. 102 | .\" 103 | .TP 104 | .B "\--preload" 105 | By default the indices contained in the 106 | .B .esi 107 | file, and the sequences referenced in the corresponding 108 | .B .esd 109 | file are loaded into memory when the server is started. 110 | This is necessary to achieve fast performance 111 | that would otherwise be hampered by frequent disk accesses. 112 | This option allows the index and sequence preloading to be turned 113 | off, which allows the server to run much more slowly, 114 | but with faster startup and a smaller memory footprint. 115 | It is not advised to turn preloading off unless testing or debugging 116 | the server. 117 | .\" 118 | .TP 119 | .B "\--maxconnections" 120 | The server is multithreaded. This option sets the number client processes 121 | which are allowed to connect to the server simultaneously. 122 | For good performance, it should not be set to more than the number of CPUs 123 | on the machine on which the server is running. 124 | .\" 125 | .TP 126 | .B "\--verbosity" 127 | Set the verbosity level for the server. If it is zero, the server 128 | will be silent, and the higher the number, the more messages 129 | are reported by the server about what is happening. 130 | .\" 131 | 132 | .RE 133 | .SH INTERFACE 134 | .T 135 | This section documents the communication interface between 136 | the client and server. 137 | The interface is documented for people wishing to write their own 138 | custom server to sit behind exonerate 139 | - for normal use of exonerate, it is not necessary to know this. 140 | .\" 141 | .P 142 | The interface works by the client sending simple command lines 143 | and the server sending simple reply lines over a socket. 144 | All the commands and replies are simple lines of ASCII text, 145 | so it is possible to use telnet as a client for testing a server. 146 | .\" 147 | .P 148 | Any command is a single line of text, but a reply may contain 149 | many lines of text. The replies are in the form of 150 | .B : 151 | .\" 152 | .P 153 | Any reply can include lines with the tag 154 | .B warning: 155 | or 156 | .B error: 157 | . 158 | These 159 | .B warning: 160 | and 161 | .B error: 162 | tags are echoed by the client, and the client will 163 | exit after receiving any 164 | .B error: 165 | reply. 166 | .P 167 | .\" 168 | When the server is returning a multiline reply, the first 169 | line must show the number of lines in the whole reply as: 170 | .B linecount: 171 | For examples, see the replies from the 172 | .B "get hsps" 173 | commands in the example session below. 174 | .P 175 | .\" 176 | The client will only open a single connection to any server, 177 | although a multithreaded server is obviously required to allow multiple clients 178 | to connect simultaneously. 179 | .\" 180 | .P 181 | .SS Commands and replies used in for the interface. 182 | .P 183 | .PP 184 | .PD 0 185 | .TP 10 186 | Command: 187 | .B version 188 | .TP 10 189 | Reply: 190 | version 191 | 192 | .TP 10 193 | Command: 194 | .B exit 195 | .TP 10 196 | Reply: 197 | ( no reply - server closes connection ) 198 | 199 | .TP 10 200 | Command: 201 | .B dbinfo 202 | .TP 10 203 | Reply: 204 | dbinfo: 205 | 206 | The 207 | .B dbinfo 208 | command returns information about the database loaded on the server. 209 | The returned fields are: 210 | 211 | .RS 212 | .PD 0 213 | .TP 16 214 | .B 215 | either dna or protein 216 | .TP 16 217 | .B 218 | either softmasked or unmasked 219 | .TP 16 220 | .B 221 | the number of sequences in the database 222 | .TP 16 223 | .B 224 | the length of the longest sequence in the database 225 | .TP 16 226 | .B 227 | the total length of all the sequences in the database 228 | .RE 229 | 230 | .TP 10 231 | Command: 232 | .B lookup 233 | 234 | .TP 10 235 | Reply: 236 | lookup: 237 | 238 | The lookup command is used to map an external identifier to an internal 239 | identifier. 240 | 241 | .TP 10 242 | Command: 243 | .B get info 244 | 245 | .TP 10 246 | Reply: 247 | seqinfo: [ ] 248 | 249 | The get info command returns information about a sequence in the database. 250 | The returned fields are: 251 | 252 | .RS 253 | .TP 16 254 | .B 255 | the sequence length 256 | .TP 16 257 | .B 258 | a gcg format checksum (see below) 259 | .TP 16 260 | .B 261 | the external id (eg. from fasta header) 262 | .TP 16 263 | .B 264 | a description line for the sequence (also from the fasta header), 265 | this field is optional an may be ommitted. 266 | .RE 267 | 268 | .TP 10 269 | Command: 270 | .B get seq 271 | 272 | .TP 10 273 | Reply: 274 | seq: 275 | 276 | The get seq command returns a whole sequence on one line. 277 | 278 | .TP 10 279 | Command: 280 | .B get subseq 281 | 282 | .TP 10 283 | Reply: 284 | subseq: 285 | 286 | The get subseq command returns part of a sequence. 287 | The start of the sequence is position zero. 288 | eg. get subseq 0 0 10 289 | will return the first 10 bases of the first sequence in the database. 290 | 291 | .TP 10 292 | Command: 293 | .B set query 294 | 295 | .TP 10 296 | Reply: 297 | ok: 298 | 299 | The seq query command is used to send a query sequence to the server. 300 | It returns the length of the sequence and a gcg checksum 301 | 302 | .TP 10 303 | Command: 304 | .B revcomp 305 | 306 | .TP 10 307 | Reply: 308 | ok: strand 309 | 310 | The revcomp query command makes the server 311 | reverse complement the query. This is to save the bandwidth 312 | of sending the query twice. 313 | 314 | The revcomp target command is to tell the server 315 | to treat the database as its reverse complement. 316 | The client only sends this command when searching a translated 317 | database, so need not be implemented for most types of search. 318 | 319 | .TP 10 320 | Command: 321 | .B set param 322 | 323 | .TP 10 324 | Reply: 325 | ok: 326 | 327 | The set parameter command sends parameters from the exonerate command line 328 | to the server. This commands can all be ignored by the client for a basic 329 | implementation, but cannot be ignored for optimal performance. 330 | 331 | .TP 10 332 | Command: 333 | .B get hsps 334 | .TP 10 335 | Reply: 336 | hspset: { } 337 | .TP 10 338 | Or: 339 | hspset: empty 340 | 341 | The get hsps command is the main command for getting sets of hsps. 342 | The server may return multiple hspsets. 343 | The returned fields are: 344 | 345 | .RS 346 | .TP 16 347 | .B 348 | The internal id of the target sequence for these HSPsets. 349 | .TP 16 350 | .B 351 | The hsp query start position 352 | .TP 16 353 | .B 354 | The hsp target start position 355 | .TP 16 356 | .B 357 | The hsp length 358 | .RE 359 | 360 | .RS 361 | The last three fields represent an HSP, and may be repeated many times 362 | on one 363 | .B hspset: 364 | reply line. 365 | .RE 366 | .PD 367 | .PP 368 | .\" 369 | .SS A simple example client server dialog. 370 | .P 371 | .PP 372 | .nf 373 | .SP 374 | 375 | % telnet localhost 12886 376 | Trying 127.0.0.1... 377 | Connected to localhost.localdomain. 378 | Escape character is '^]'. 379 | % version 380 | version: exonerate-server 2.0.0 381 | % dbinfo 382 | dbinfo: dna softmasked 100000 1701 38113579 383 | % lookup AA159529.1 384 | lookup: 88065 385 | % get info 88065 386 | seqinfo: 62 2028 AA159529.1 zo72g05.s1 Stratagene pancreas (#937208) Homo sapiens cDNA 387 | % get seq 88065 388 | seq: NAACTCATCNTTTTCTGCTGNATCCTCTTCACCAGTTTGGGGGANGGCCTGCACTTCCANAG 389 | % get subseq 88065 10 20 390 | subseq: TTTTCTGCTGNATCCTCTTC 391 | % set query NAACTCATCNTTTTCTGCTGNATCCTCTTCACCAGTTTGGGGGANGGCCTGCACTTCCANAG 392 | ok: 62 2028 393 | % get hsps 394 | linecount: 15 395 | hspset: 12423 1 349 41 396 | hspset: 44900 1 356 47 397 | hspset: 61781 1 358 41 36 392 26 398 | hspset: 70065 1 349 41 36 383 26 399 | hspset: 88065 1 1 61 400 | hspset: 91032 1 357 41 36 391 26 401 | hspset: 91442 1 350 41 36 384 26 402 | hspset: 92971 1 348 41 36 382 26 403 | hspset: 94311 1 375 41 404 | hspset: 95381 1 346 41 36 380 26 405 | hspset: 96808 10 385 32 36 410 26 406 | hspset: 88449 18 11 22 407 | hspset: 91036 6 6 56 408 | hspset: 93736 36 400 26 409 | % revcomp query 410 | ok: query strand revcomp 411 | % get hsps 412 | linecount: 6 413 | hspset: 12564 0 64 26 20 83 41 414 | hspset: 61780 0 266 61 415 | hspset: 29148 0 116 61 416 | hspset: 25849 15 445 22 417 | hspset: 93938 26 265 34 418 | % exit 419 | Connection closed by foreign host. 420 | .SP 421 | .fi 422 | 423 | .\" 424 | .SH ENVIRONMENT 425 | Not documented yet. 426 | .\" 427 | .SH EXAMPLES 428 | .\" 429 | .B 1. 430 | Example of creating a translated index 431 | and running a fast protein2genome search using exonerate-server 432 | 433 | .B fasta2esd 434 | human.genomic.fasta human.genomic.esd 435 | .B esd2esi 436 | --translate yes human.genomic.esd human.genomic.trans.esi 437 | .B exonerate-server 438 | --port 1234 human.genomic.trans.esi 439 | .B exonerate 440 | pep.fasta localhost:1234 --model p2g --seedrepeat 3 --geneseed 250 441 | 442 | .\" 443 | .RE 444 | .SH VERSION 445 | This documentation accompanies version 2.2.0 of the exonerate package. 446 | .\" 447 | .SH AUTHOR 448 | Guy St.C. Slater. . 449 | .L 450 | See the AUTHORS file accompanying the source code 451 | for a list of contributors. 452 | .SH AVAILABILITY 453 | This source code for the exonerate package is available 454 | under the terms of the GNU 455 | .I general 456 | public licence. 457 | 458 | Please see the file COPYING which was distrubuted with this package, 459 | or http://www.gnu.org/licenses/gpl.txt for details. 460 | 461 | This package has been developed as part of the ensembl project. 462 | Please see http://www.ensembl.org/ for more information. 463 | .SH "SEE ALSO" 464 | .BR exonerate (1), 465 | -------------------------------------------------------------------------------- /exonerate/exonerate_macos/share/man/man1/exonerate-server.1: -------------------------------------------------------------------------------- 1 | .\" Exonerate man Page 2 | .TH exonerate-server 1 "January 2008" exonerate-server "sequence comparison server" 3 | .SH NAME 4 | .\" 5 | exonerate-server \- a sequence comparison server for exonerate 6 | .\" 7 | 8 | .SH SYNOPSIS 9 | .B exonerate-server [ options ] 10 | .\" 11 | 12 | .SH DESCRIPTION 13 | .BR exonerate-server 14 | is a multi-threaded server for the exonerate sequence alignment program. 15 | 16 | It uses a set of sequences and a corresponding index file 17 | to allow fast of large datasets. 18 | .\" 19 | 20 | .RE 21 | .SH OVERVIEW 22 | .T 23 | .\" 24 | Firstly, an 25 | .B .esd 26 | file must be made from the sequence files. 27 | The 28 | .B .esd 29 | file is an Exonerate Sequence Dataset 30 | file, and can be used to group together any set 31 | of sequences where each sequences containing unique identifiers. 32 | This is done by using the 33 | .B fasta2esd 34 | utility. 35 | .RS 36 | .TP 37 | .B "fasta2esd genome.fasta genome.esd" 38 | .P 39 | .RE 40 | Next, an 41 | .B .esi 42 | file my be made from the 43 | .B .esd 44 | file. 45 | The 46 | .B .esi 47 | file is an Exonerate Sequence Index 48 | file, and contains an index or set of indices corresponding 49 | to a particular dataset. 50 | This is done by using the 51 | .B esd2esi 52 | utility. 53 | .\" 54 | .RS 55 | .TP 56 | .B "esd2esi genome.esd genome.esi" 57 | .P 58 | .RE 59 | Once the 60 | .B .esi 61 | file has been generated, the exonerate-server may be started. 62 | .RS 63 | .TP 64 | .B "exonerate-server genome.esi" 65 | .P 66 | .RE 67 | While the server is running, exonerate may be used to query 68 | the server by replacing the target sequences in the command line 69 | with the name of the server and port number. 70 | The default port number for the exonerate-server is 12886. 71 | .RS 72 | .TP 73 | .B "exonerate query.fasta localhost:12886" 74 | .P 75 | .RE 76 | 77 | .RE 78 | .SH OPTIONS 79 | .T 80 | Some of the command line options for the exonerate-server are the same as for the 81 | exonerate client, and these are documented in the man page for 82 | .B exonerate. 83 | The other options which are specific to 84 | .B exonerate-server 85 | are documented here. 86 | .TP 87 | .B "\--port" 88 | Specify the port on which the server should listen. 89 | By default, 90 | .B exonerate-server 91 | will listen on port 12886, but alternative ports may be specified with this 92 | option. 93 | .\" 94 | .TP 95 | .B "\--input" 96 | Specify the index file to be used when the server is started. 97 | This option is mandatory. The index file is a 98 | .B .esi 99 | file generated by the 100 | .B esd2esi 101 | utility. 102 | .\" 103 | .TP 104 | .B "\--preload" 105 | By default the indices contained in the 106 | .B .esi 107 | file, and the sequences referenced in the corresponding 108 | .B .esd 109 | file are loaded into memory when the server is started. 110 | This is necessary to achieve fast performance 111 | that would otherwise be hampered by frequent disk accesses. 112 | This option allows the index and sequence preloading to be turned 113 | off, which allows the server to run much more slowly, 114 | but with faster startup and a smaller memory footprint. 115 | It is not advised to turn preloading off unless testing or debugging 116 | the server. 117 | .\" 118 | .TP 119 | .B "\--maxconnections" 120 | The server is multithreaded. This option sets the number client processes 121 | which are allowed to connect to the server simultaneously. 122 | For good performance, it should not be set to more than the number of CPUs 123 | on the machine on which the server is running. 124 | .\" 125 | .TP 126 | .B "\--verbosity" 127 | Set the verbosity level for the server. If it is zero, the server 128 | will be silent, and the higher the number, the more messages 129 | are reported by the server about what is happening. 130 | .\" 131 | 132 | .RE 133 | .SH INTERFACE 134 | .T 135 | This section documents the communication interface between 136 | the client and server. 137 | The interface is documented for people wishing to write their own 138 | custom server to sit behind exonerate 139 | - for normal use of exonerate, it is not necessary to know this. 140 | .\" 141 | .P 142 | The interface works by the client sending simple command lines 143 | and the server sending simple reply lines over a socket. 144 | All the commands and replies are simple lines of ASCII text, 145 | so it is possible to use telnet as a client for testing a server. 146 | .\" 147 | .P 148 | Any command is a single line of text, but a reply may contain 149 | many lines of text. The replies are in the form of 150 | .B : 151 | .\" 152 | .P 153 | Any reply can include lines with the tag 154 | .B warning: 155 | or 156 | .B error: 157 | . 158 | These 159 | .B warning: 160 | and 161 | .B error: 162 | tags are echoed by the client, and the client will 163 | exit after receiving any 164 | .B error: 165 | reply. 166 | .P 167 | .\" 168 | When the server is returning a multiline reply, the first 169 | line must show the number of lines in the whole reply as: 170 | .B linecount: 171 | For examples, see the replies from the 172 | .B "get hsps" 173 | commands in the example session below. 174 | .P 175 | .\" 176 | The client will only open a single connection to any server, 177 | although a multithreaded server is obviously required to allow multiple clients 178 | to connect simultaneously. 179 | .\" 180 | .P 181 | .SS Commands and replies used in for the interface. 182 | .P 183 | .PP 184 | .PD 0 185 | .TP 10 186 | Command: 187 | .B version 188 | .TP 10 189 | Reply: 190 | version 191 | 192 | .TP 10 193 | Command: 194 | .B exit 195 | .TP 10 196 | Reply: 197 | ( no reply - server closes connection ) 198 | 199 | .TP 10 200 | Command: 201 | .B dbinfo 202 | .TP 10 203 | Reply: 204 | dbinfo: 205 | 206 | The 207 | .B dbinfo 208 | command returns information about the database loaded on the server. 209 | The returned fields are: 210 | 211 | .RS 212 | .PD 0 213 | .TP 16 214 | .B 215 | either dna or protein 216 | .TP 16 217 | .B 218 | either softmasked or unmasked 219 | .TP 16 220 | .B 221 | the number of sequences in the database 222 | .TP 16 223 | .B 224 | the length of the longest sequence in the database 225 | .TP 16 226 | .B 227 | the total length of all the sequences in the database 228 | .RE 229 | 230 | .TP 10 231 | Command: 232 | .B lookup 233 | 234 | .TP 10 235 | Reply: 236 | lookup: 237 | 238 | The lookup command is used to map an external identifier to an internal 239 | identifier. 240 | 241 | .TP 10 242 | Command: 243 | .B get info 244 | 245 | .TP 10 246 | Reply: 247 | seqinfo: [ ] 248 | 249 | The get info command returns information about a sequence in the database. 250 | The returned fields are: 251 | 252 | .RS 253 | .TP 16 254 | .B 255 | the sequence length 256 | .TP 16 257 | .B 258 | a gcg format checksum (see below) 259 | .TP 16 260 | .B 261 | the external id (eg. from fasta header) 262 | .TP 16 263 | .B 264 | a description line for the sequence (also from the fasta header), 265 | this field is optional an may be ommitted. 266 | .RE 267 | 268 | .TP 10 269 | Command: 270 | .B get seq 271 | 272 | .TP 10 273 | Reply: 274 | seq: 275 | 276 | The get seq command returns a whole sequence on one line. 277 | 278 | .TP 10 279 | Command: 280 | .B get subseq 281 | 282 | .TP 10 283 | Reply: 284 | subseq: 285 | 286 | The get subseq command returns part of a sequence. 287 | The start of the sequence is position zero. 288 | eg. get subseq 0 0 10 289 | will return the first 10 bases of the first sequence in the database. 290 | 291 | .TP 10 292 | Command: 293 | .B set query 294 | 295 | .TP 10 296 | Reply: 297 | ok: 298 | 299 | The seq query command is used to send a query sequence to the server. 300 | It returns the length of the sequence and a gcg checksum 301 | 302 | .TP 10 303 | Command: 304 | .B revcomp 305 | 306 | .TP 10 307 | Reply: 308 | ok: strand 309 | 310 | The revcomp query command makes the server 311 | reverse complement the query. This is to save the bandwidth 312 | of sending the query twice. 313 | 314 | The revcomp target command is to tell the server 315 | to treat the database as its reverse complement. 316 | The client only sends this command when searching a translated 317 | database, so need not be implemented for most types of search. 318 | 319 | .TP 10 320 | Command: 321 | .B set param 322 | 323 | .TP 10 324 | Reply: 325 | ok: 326 | 327 | The set parameter command sends parameters from the exonerate command line 328 | to the server. This commands can all be ignored by the client for a basic 329 | implementation, but cannot be ignored for optimal performance. 330 | 331 | .TP 10 332 | Command: 333 | .B get hsps 334 | .TP 10 335 | Reply: 336 | hspset: { } 337 | .TP 10 338 | Or: 339 | hspset: empty 340 | 341 | The get hsps command is the main command for getting sets of hsps. 342 | The server may return multiple hspsets. 343 | The returned fields are: 344 | 345 | .RS 346 | .TP 16 347 | .B 348 | The internal id of the target sequence for these HSPsets. 349 | .TP 16 350 | .B 351 | The hsp query start position 352 | .TP 16 353 | .B 354 | The hsp target start position 355 | .TP 16 356 | .B 357 | The hsp length 358 | .RE 359 | 360 | .RS 361 | The last three fields represent an HSP, and may be repeated many times 362 | on one 363 | .B hspset: 364 | reply line. 365 | .RE 366 | .PD 367 | .PP 368 | .\" 369 | .SS A simple example client server dialog. 370 | .P 371 | .PP 372 | .nf 373 | .SP 374 | 375 | % telnet localhost 12886 376 | Trying 127.0.0.1... 377 | Connected to localhost.localdomain. 378 | Escape character is '^]'. 379 | % version 380 | version: exonerate-server 2.0.0 381 | % dbinfo 382 | dbinfo: dna softmasked 100000 1701 38113579 383 | % lookup AA159529.1 384 | lookup: 88065 385 | % get info 88065 386 | seqinfo: 62 2028 AA159529.1 zo72g05.s1 Stratagene pancreas (#937208) Homo sapiens cDNA 387 | % get seq 88065 388 | seq: NAACTCATCNTTTTCTGCTGNATCCTCTTCACCAGTTTGGGGGANGGCCTGCACTTCCANAG 389 | % get subseq 88065 10 20 390 | subseq: TTTTCTGCTGNATCCTCTTC 391 | % set query NAACTCATCNTTTTCTGCTGNATCCTCTTCACCAGTTTGGGGGANGGCCTGCACTTCCANAG 392 | ok: 62 2028 393 | % get hsps 394 | linecount: 15 395 | hspset: 12423 1 349 41 396 | hspset: 44900 1 356 47 397 | hspset: 61781 1 358 41 36 392 26 398 | hspset: 70065 1 349 41 36 383 26 399 | hspset: 88065 1 1 61 400 | hspset: 91032 1 357 41 36 391 26 401 | hspset: 91442 1 350 41 36 384 26 402 | hspset: 92971 1 348 41 36 382 26 403 | hspset: 94311 1 375 41 404 | hspset: 95381 1 346 41 36 380 26 405 | hspset: 96808 10 385 32 36 410 26 406 | hspset: 88449 18 11 22 407 | hspset: 91036 6 6 56 408 | hspset: 93736 36 400 26 409 | % revcomp query 410 | ok: query strand revcomp 411 | % get hsps 412 | linecount: 6 413 | hspset: 12564 0 64 26 20 83 41 414 | hspset: 61780 0 266 61 415 | hspset: 29148 0 116 61 416 | hspset: 25849 15 445 22 417 | hspset: 93938 26 265 34 418 | % exit 419 | Connection closed by foreign host. 420 | .SP 421 | .fi 422 | 423 | .\" 424 | .SH ENVIRONMENT 425 | Not documented yet. 426 | .\" 427 | .SH EXAMPLES 428 | .\" 429 | .B 1. 430 | Example of creating a translated index 431 | and running a fast protein2genome search using exonerate-server 432 | 433 | .B fasta2esd 434 | human.genomic.fasta human.genomic.esd 435 | .B esd2esi 436 | --translate yes human.genomic.esd human.genomic.trans.esi 437 | .B exonerate-server 438 | --port 1234 human.genomic.trans.esi 439 | .B exonerate 440 | pep.fasta localhost:1234 --model p2g --seedrepeat 3 --geneseed 250 441 | 442 | .\" 443 | .RE 444 | .SH VERSION 445 | This documentation accompanies version 2.2.0 of the exonerate package. 446 | .\" 447 | .SH AUTHOR 448 | Guy St.C. Slater. . 449 | .L 450 | See the AUTHORS file accompanying the source code 451 | for a list of contributors. 452 | .SH AVAILABILITY 453 | This source code for the exonerate package is available 454 | under the terms of the GNU 455 | .I general 456 | public licence. 457 | 458 | Please see the file COPYING which was distrubuted with this package, 459 | or http://www.gnu.org/licenses/gpl.txt for details. 460 | 461 | This package has been developed as part of the ensembl project. 462 | Please see http://www.ensembl.org/ for more information. 463 | .SH "SEE ALSO" 464 | .BR exonerate (1), 465 | -------------------------------------------------------------------------------- /statics/js/result.js: -------------------------------------------------------------------------------- 1 | process.env['ELECTRON_DISABLE_SECURITY_WARNINGS'] = 'true'; 2 | //const {remote} = require('electron'); 3 | const {dialog} = require('electron').remote; 4 | const fs = require("fs"); 5 | const func = require('./func'); 6 | 7 | var dom_gene = document.getElementById("container_gene"); 8 | var Chart_gene = echarts.init(dom_gene); 9 | var info, output_info; 10 | 11 | 12 | $(document).ready(function(){ 13 | 14 | ipcRenderer.send('get_data'); 15 | ipcRenderer.on('send_data', function (event, data) { 16 | info = data[0]; 17 | output_info = data[1]; 18 | if (info.category.length === 3){ 19 | alert('Oops... NO suited gRNA found!') 20 | } 21 | showgene(info.all_info, info.dna_len, info.category) 22 | }); 23 | 24 | var clickNumber = 0; 25 | $('#reverse').click(function () { 26 | if (clickNumber % 2 ===0){ 27 | showgene(info_r.all_info, info_r.dna_len, info_r.category) 28 | }else { 29 | showgene(info.all_info, info.dna_len, info.category) 30 | } 31 | clickNumber ++; 32 | }); 33 | 34 | 35 | $(window).resize(function () { 36 | $("#container_gene").attr({"width": $(window).width(), 37 | "height": $(window).height() - 200 38 | }); 39 | // $("#container_gene") 40 | }) 41 | 42 | }); 43 | 44 | 45 | function renderItem(params, api) { 46 | 47 | var categoryIndex = api.value(0); 48 | 49 | 50 | var start = api.coord([api.value(1), categoryIndex]); 51 | var end = api.coord([api.value(2), categoryIndex]); 52 | var name_label = api.value(3); 53 | 54 | if (api.value(4) === '#959ca3'){ 55 | var height = api.size([0, 1])[1] * 0.05; 56 | } 57 | else { 58 | var height = api.size([0, 1])[1] * 0.2; 59 | } 60 | 61 | 62 | 63 | 64 | var rectShape = echarts.graphic.clipRectByRect({ 65 | x: start[0], 66 | y: start[1] - height / 2, 67 | width: end[0] - start[0], 68 | height: height 69 | }, { 70 | x: params.coordSys.x, 71 | y: params.coordSys.y, 72 | width: params.coordSys.width, 73 | height: params.coordSys.height 74 | }); 75 | 76 | return rectShape && { 77 | type: 'rect', 78 | shape: rectShape, 79 | style: api.style() 80 | }; 81 | } 82 | 83 | 84 | option = { 85 | 86 | 87 | legend:{ 88 | left:30, 89 | right:30 90 | }, 91 | 92 | toolbox: { 93 | itemSize:25, 94 | itemGap:15, 95 | right:30, 96 | feature: { 97 | saveAsImage: { 98 | title: 'save result as png', 99 | icon:'image://statics/img/photo.png', 100 | pixelRatio:2 101 | }, 102 | myTool1: { 103 | show: true, 104 | title: 'save result as file', 105 | icon: 'image://statics/img/file.png', 106 | onclick: function (){ 107 | 108 | filename = dialog.showSaveDialog({} 109 | ).then(result => { 110 | filename = result.filePath; 111 | if (filename === undefined) { 112 | alert('the user clicked the btn but didn\'t created a file'); 113 | return; 114 | } 115 | fs.writeFile(filename, func.savefile(output_info), (err) => { 116 | if (err) { 117 | alert('an error ocurred with file creation ' + err.message); 118 | return 119 | } 120 | alert('CREATED FILE SUCCESFULLY!'); 121 | }) 122 | }).catch(err => { 123 | alert(err) 124 | }) 125 | 126 | } 127 | }, 128 | } 129 | }, 130 | 131 | tooltip: { 132 | 133 | axisPointer: { 134 | type: 'cross', 135 | }, 136 | confine: true, 137 | 138 | formatter: function (params) { 139 | 140 | var start_num = Number(params.value[1])+1; 141 | if (params.name === "DNA" && params.value[4] === '#c5cfd8'){ 142 | return params.marker + params.name + ': ' + params.value[3] + ' ' +params.value[2] ; 143 | }else if(params.name === "CDS"){ 144 | return params.marker + params.value[3] + ": " + start_num + "-" + params.value[2]; 145 | }else if(params.name === "DNA" && params.value[4] === '#389438'){ 146 | return params.marker + "target codon" + params.value[6] + ": " + params.value[5] + " " + params.value[7] + "-" + params.value[8] 147 | } else if(params.name.indexOf("g") !== -1){ 148 | 149 | offtarget_info = ''; 150 | if (typeof (params.value[8]) === "string"){ 151 | offtarget_info = params.value[8] + ' (mismatch0-mismatch1-mismatch2-mismatch3)' 152 | } 153 | else if (params.value[8] == null){ 154 | offtarget_info = 'No gRNA offtarget information' 155 | } 156 | // else { 157 | // for(let i=0; i<=5; i++){ 158 | // if (String(i) in params.value[8]){ 159 | // if (i===0){ 160 | // offtarget_info += 'mismatch'+ String(i) + ':' + String(Number(params.value[8][i][0])-1) + '(' + String(Number(params.value[8][i][1]-1)) + ')' + "
" 161 | // } 162 | // else { offtarget_info += 'mismatch'+ String(i) + ':' + params.value[8][i][0]+'('+params.value[8][i][1]+')' + "
"} 163 | // 164 | // } 165 | // } 166 | // } 167 | 168 | // offtarget_example = 'mismatch1:5(2) means in genome-wide mismatch one base is allowed have 5 same site,' + "
" +'The Numbers in parentheses is 2 out of 5 overlap with gene CDS, The lower the number the better' 169 | 170 | var gRNA_seqeunce = " gRNA sequence: " + ' ' + params.value[9][0] + "
"; 171 | var gRNA_position = " gRNA position: " + ' ' +Number(params.value[9][1]+1) + "-" + params.value[9][2] + " strand:" + params.value[5] + "
"; 172 | var target_info = " Target codon: " + ' ' + params.value[7][3] + " " + params.value[7][0] + " " + (Number(params.value[7][1]) + 1) + "-" + params.value[7][2] + "
"; 173 | var editing_position = " Editing position: " + ' ' + params.value[6] + "
" 174 | offtarget_info = " Offtarget info: " + offtarget_info; 175 | // offtarget_example = " example: "+ offtarget_example; 176 | 177 | return gRNA_seqeunce + "
" + gRNA_position + "
" + target_info + "
" + editing_position + "
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' 331 | // } 332 | // info += (Number(i)+1) + '. ' + 'editor: ' + params.value[7][i]['editor'] + '
' + 'ref:' + ''+ params.value[7][i]['ref']+ '' + '
' + 'edit_window:' + params.value[7][i]['window'][0] + '-' + params.value[7][i]['window'][1] 333 | // } 334 | // 335 | // if ($("#grna_info").css('display') === 'none'){ 336 | // $("#editor").html(info); 337 | // $("#grna_info").slideDown('slow') 338 | // }else { 339 | // $("#grna_info").slideUp('slow'); 340 | // $("#editor").html(info); 341 | // $("#grna_info").slideDown('slow') 342 | // } 343 | // 344 | // 345 | // } 346 | //}); 347 | 348 | 349 | function datazoom_location() { 350 | 351 | var from_num = Number(document.getElementById("from").value); 352 | var end_num = Number(document.getElementById("end").value); 353 | 354 | if (option && typeof option ==="object"){ 355 | option["dataZoom"][0]["start"] = (from_num / info.dna_len) *100; 356 | option["dataZoom"][0]["end"] = (end_num / info.dna_len) *100; 357 | Chart_gene.setOption(option, true); 358 | } 359 | 360 | } 361 | 362 | // 监听缩放事件 363 | i = 0; 364 | Chart_gene.on('dataZoom', function (para) { 365 | 366 | if ((para['batch'][0]['end'] - para['batch'][0]['start']) * info.dna_len / 100 < 120 && i===0){ 367 | option["series"][0]["label"]['normal']['show'] = true; 368 | option["dataZoom"][0]["start"] = para['batch'][0]['start']; 369 | option["dataZoom"][0]["end"] = para['batch'][0]['end']; 370 | Chart_gene.setOption(option, true); 371 | i+=1 372 | } 373 | if ((para['batch'][0]['end'] - para['batch'][0]['start']) * info.dna_len / 100 > 150 && i===1){ 374 | option["series"][0]["label"]['normal']['show'] = false; 375 | option["dataZoom"][0]["start"] = para['batch'][0]['start']; 376 | option["dataZoom"][0]["end"] = para['batch'][0]['end']; 377 | Chart_gene.setOption(option, true); 378 | i-=1 379 | } 380 | 381 | }); 382 | 383 | 384 | // 图表结果随着页面大小自动调整 385 | setTimeout(function (){ 386 | window.onresize = function () { 387 | Chart_gene.resize(); 388 | } 389 | },200) 390 | 391 | 392 | 393 | 394 | 395 | -------------------------------------------------------------------------------- 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CTGCGGCTT",19900,19920,"-"]},{"codon":["CAG",20141,20144],"grna1":["CCTGGACCTGGATGCGCAGCAGG",20125,20145,"+"],"grna2":["GGATGCGCAGCAGGCCCGCGTGG",20134,20154,"+"],"grna3":["GATGCGCAGCAGGCCCGCGTGGG",20135,20155,"+"]},{"codon":["CAG",20144,20147],"grna1":["CCTGGACCTGGATGCGCAGCAGG",20125,20145,"+"],"grna2":["GGATGCGCAGCAGGCCCGCGTGG",20134,20154,"+"],"grna3":["GATGCGCAGCAGGCCCGCGTGGG",20135,20155,"+"],"grna4":["AGCAGGCCCGCGTGGGCCAGTGG",20142,20162,"+"]},{"codon":["CAG",20159,20162],"grna1":["AGCAGGCCCGCGTGGGCCAGTGG",20142,20162,"+"],"grna2":["CCAGTGGCTGCTGCTCTTCCTGG",20158,20178,"+"],"grna3":["CAGTGGCTGCTGCTCTTCCTGGG",20159,20179,"+"]},{"codon":["TGG",20162,20165],"grna1":["GGGCGCACCCGGTCACCGACGAC",20151,20171,"-"],"grna2":["GGCGCACCCGGTCACCGACGACG",20152,20172,"-"],"grna3":["GGTCACCGACGACGAGAAGGACC",20161,20181,"-"]},{"codon":["CAG",20216,20219],"grna1":["CCACCCTGGGCCTCAGCCAGCGG",20199,20219,"+"]},{"codon":["CAG",20270,20273],"grna1":["CACTCCCACGGGCCCCAGTTCGG",20255,20275,"+"],"grna2":["CGGGCCCCAGTTCGGCTCCGAGG",20263,20283,"+"],"grna3":["GCCCCAGTTCGGCTCCGAGGTGG",20266,20286,"+"]}] 2 | -------------------------------------------------------------------------------- /statics/js/main.js: -------------------------------------------------------------------------------- 1 | // process.env['ELECTRON_DISABLE_SECURITY_WARNINGS'] = 'true'; 2 | var form_info = {'isform': 1, 'dna_sequence':'', 'cds_sequence':'', 'pam':'', 'grna_length':'', 'DS': false, 'DF':false, 'CS':false, 'CF':false, 'FA':false, 'database':''}; 3 | const snapgeneToJson = require('bio-parsers').snapgeneToJson; 4 | const fs = require("fs"); 5 | const wget = require('wget-improved'); 6 | const func = require('./func'); 7 | 8 | 9 | $(document).ready(function(){ 10 | 11 | 12 | ipcRenderer.send('get_app_path', ''); 13 | 14 | ipcRenderer.on('send_app_path', function (event, data) { 15 | app_path = data 16 | 17 | fs.readdir(app_path + '/offtarget_info/', function (err, files) { 18 | if (err) {console.log('read file direction failed')} 19 | else { 20 | for (let i in files){ 21 | if (files[i].indexOf('json') != -1) { 22 | $("#offtarget").append(""); 23 | } 24 | } 25 | 26 | // 向index.html中添加需要下载的offtarget数据 27 | // var no_download = func.list_subtract(all_database, files); 28 | // for (let i in no_download){ 29 | // if (no_download[i] === 'os_cas9_ngg_20_offtarget_info.json'){ 30 | // $("#download").append("\"\"") 31 | // } 32 | // 33 | // else if (no_download[i] === 'os_cas12_tttv_23_offtarget_info.json'){ 34 | // $("#download").append("\"\"") 35 | // } 36 | // } 37 | } 38 | }); 39 | 40 | }); 41 | 42 | 43 | $("#genbank_option").click(function () { 44 | if($("#snapgene_content").css("display")==='block') { 45 | $("#snapgene_content").slideToggle("slow"); 46 | } 47 | if($("#fasta_content").css("display")==='block') { 48 | $("#fasta_content").slideToggle("slow"); 49 | } 50 | if($("#genbank_content").css("display")==='none') { 51 | $("#genbank_content").slideToggle("slow"); 52 | } 53 | 54 | $('#gb_file').prop("disabled", false); 55 | $('#isoform_num').prop("disabled", false); 56 | $('#sg_file').prop("disabled", true); 57 | $('#isoform_num2').prop("disabled", true); 58 | $('#dna_file').prop("disabled", true); 59 | $('#dna_sequence').prop("disabled", true); 60 | $('#cds_file').prop("disabled", true); 61 | $('#cds_sequence').prop("disabled", true); 62 | $('#sg_file').val(''); 63 | $('#sg_file_label').html('Load SnapGene file'); 64 | $('#isoform_num2').val(''); 65 | $('#dna_sequence').val(''); 66 | $('#cds_sequence').val(''); 67 | $('#dna_file').val(''); 68 | $('#dna_file_label').html('Load DNA Fasta file'); 69 | $('#cds_file').val(''); 70 | $('#cds_file_label').html('Load CDS Fasta file'); 71 | }); 72 | 73 | $("#snapgene_option").click(function () { 74 | if($("#genbank_content").css("display")==='block'){ 75 | $("#genbank_content").slideToggle("slow"); 76 | } 77 | if($("#fasta_content").css("display")==='block') { 78 | $("#fasta_content").slideToggle("slow"); 79 | } 80 | if($("#snapgene_content").css("display")==='none') { 81 | $("#snapgene_content").slideToggle("slow"); 82 | } 83 | 84 | $('#sg_file').prop("disabled", false); 85 | $('#isoform_num2').prop("disabled", false); 86 | $('#gb_file').prop("disabled", true); 87 | $('#isoform_num').prop("disabled", true); 88 | $('#dna_file').prop("disabled", true); 89 | $('#dna_sequence').prop("disabled", true); 90 | $('#cds_file').prop("disabled", true); 91 | $('#cds_sequence').prop("disabled", true); 92 | $('#gb_file').val(''); 93 | $('#gb_file_label').html('Load GenBank file'); 94 | $('#isoform_num').val(''); 95 | $('#dna_sequence').val(''); 96 | $('#cds_sequence').val(''); 97 | $('#dna_file').val(''); 98 | $('#dna_file_label').html('Load DNA Fasta file'); 99 | $('#cds_file').val(''); 100 | $('#cds_file_label').html('Load CDS Fasta file'); 101 | }); 102 | 103 | $("#fasta_option").click(function () { 104 | if($("#genbank_content").css("display")==='block'){ 105 | $("#genbank_content").slideToggle("slow"); 106 | } 107 | if($("#snapgene_content").css("display")==='block') { 108 | $("#snapgene_content").slideToggle("slow"); 109 | } 110 | if($("#fasta_content").css("display")==='none') { 111 | $("#fasta_content").slideToggle("slow"); 112 | } 113 | 114 | $('#dna_file').prop("disabled", false); 115 | $('#dna_sequence').prop("disabled", false); 116 | $('#cds_file').prop("disabled", false); 117 | $('#cds_sequence').prop("disabled", false); 118 | $('#gb_file').prop("disabled", true); 119 | $('#isoform_num').prop("disabled", true); 120 | $('#sg_file').prop("disabled", true); 121 | $('#isoform_num2').prop("disabled", true); 122 | $('#gb_file').val(''); 123 | $('#gb_file_label').html('Load GenBank file'); 124 | $('#isoform_num').val(''); 125 | $('#sg_file').val(''); 126 | $('#sg_file_label').html('Load SnapGene file'); 127 | $('#isoform_num2').val(''); 128 | }); 129 | 130 | $("#download_btn").click(function () { 131 | $("#spinner").slideToggle("slow") 132 | }); 133 | 134 | 135 | $("#myCanvas1").attr({"width": $(".title").width()-300, 136 | "height": 30 137 | }); 138 | var c1=document.getElementById("myCanvas1"); 139 | var ctx1=c1.getContext("2d"); 140 | ctx1.moveTo(0,15); 141 | ctx1.lineTo($(".title").width()-300,15); 142 | ctx1.stroke(); 143 | 144 | 145 | $("#myCanvas2").attr({"width": $(".title").width()-300, 146 | "height": 30 147 | }); 148 | var c2=document.getElementById("myCanvas2"); 149 | var ctx2=c2.getContext("2d"); 150 | ctx2.moveTo(0,15); 151 | ctx2.lineTo($(".title").width()-300,15); 152 | ctx2.stroke(); 153 | 154 | 155 | $(window).resize(function () { 156 | 157 | $("#myCanvas1").attr({"width": $(".title").width()-300, 158 | "height": 30 159 | }); 160 | var c1=document.getElementById("myCanvas1"); 161 | var ctx1=c1.getContext("2d"); 162 | ctx1.moveTo(0,15); 163 | ctx1.lineTo($(".title").width()-300,15); 164 | ctx1.stroke(); 165 | 166 | 167 | $("#myCanvas2").attr({"width": $(".title").width()-300, 168 | "height": 30 169 | }); 170 | var c2=document.getElementById("myCanvas2"); 171 | var ctx2=c2.getContext("2d"); 172 | ctx2.moveTo(0,15); 173 | ctx2.lineTo($(".title").width()-300,15); 174 | ctx2.stroke(); 175 | }); 176 | 177 | $("#gb_file").bind("change",function () { 178 | $('#gb_file_label').text(this.files[0]['name']) 179 | }); 180 | 181 | $("#sg_file").bind("change",function () { 182 | $('#sg_file_label').text(this.files[0]['name']) 183 | }); 184 | 185 | $("#dna_file").bind("change",function () { 186 | $('#dna_file_label').text(this.files[0]['name']) 187 | }); 188 | 189 | $("#cds_file").bind("change",function () { 190 | $('#cds_file_label').text(this.files[0]['name']) 191 | }); 192 | 193 | // var value = 0; 194 | // setInterval(function(){ 195 | // if (value != 100) { 196 | // value = parseInt(value) + 1; 197 | // $("#prog").css("width", value + "%").text(value + "%"); 198 | // if (value>=0 && value<=30) { 199 | // $("#prog").addClass("progress-bar-danger"); 200 | // } else if (value>=30 && value <=60) { 201 | // $("#prog").removeClass("progress-bar-danger"); 202 | // $("#prog").addClass("progress-bar-warning"); 203 | // } else if (value>=60 && value <=90) { 204 | // $("#prog").removeClass("progress-bar-warning"); 205 | // $("#prog").addClass("progress-bar-info"); 206 | // } else if(value >= 90 && value<100) { 207 | // $("#prog").removeClass("progress-bar-info"); 208 | // $("#prog").addClass("progress-bar-success"); 209 | // } 210 | // } 211 | // }, 50); 212 | 213 | $("#genbank_option").click(function () { 214 | 215 | $("#snapgene_option").css("color","#FFFFFF"); 216 | $("#fasta_option").css("color","#FFFFFF"); 217 | $("#genbank_option").css("color","#c3325f"); 218 | 219 | }); 220 | 221 | $("#snapgene_option").click(function () { 222 | 223 | $("#genbank_option").css("color","#FFFFFF"); 224 | $("#fasta_option").css("color","#FFFFFF"); 225 | $("#snapgene_option").css("color","#c3325f"); 226 | 227 | }); 228 | 229 | $("#fasta_option").click(function () { 230 | 231 | $("#genbank_option").css("color","#FFFFFF"); 232 | $("#snapgene_option").css("color","#FFFFFF"); 233 | $("#fasta_option").css("color","#c3325f"); 234 | 235 | }); 236 | 237 | 238 | 239 | }); 240 | 241 | 242 | function analyse_isform() { 243 | var inputfile = document.getElementById('gb_file'); 244 | 245 | var file = inputfile.files[0]; 246 | 247 | var reader = new FileReader(); 248 | 249 | reader.readAsText(file,'utf8'); 250 | reader.onload = function () { 251 | ipcRenderer.send('sent_gb', this.result) 252 | }; 253 | } 254 | 255 | function analyse_isform2(file) { 256 | let isoform_num = 0; 257 | const options = { 258 | fileName: "example.fa", //the filename is used if none is found in the genbank 259 | isProtein: false, //if you know that it is a protein string being parsed you can pass true here 260 | //genbankToJson options only 261 | inclusive1BasedStart: false, //by default feature starts are parsed out as 0-based and inclusive 262 | inclusive1BasedEnd: false, //by default feature ends are parsed out as 0-based and inclusive 263 | acceptParts: true //by default features with a feature.notes.pragma[0] === "Teselagen_Part" are added to the sequenceData.parts array. Setting this to false will keep them as features instead 264 | }; 265 | 266 | snapgeneToJson(file, function(result) { 267 | $('#isoform_num2').empty(); 268 | for (let i in result[0]['parsedSequence']['features']){ 269 | if (result[0]['parsedSequence']['features'][i]['type'] === 'CDS'){ 270 | isoform_num += 1; 271 | $("#isoform_num2").append("\"\"") 272 | } 273 | } 274 | 275 | ipcRenderer.send('sent_sg', result) 276 | },options); 277 | 278 | 279 | } 280 | 281 | 282 | function read_dna_fa() { 283 | var inputfile = document.getElementById('dna_file'); 284 | 285 | var file = inputfile.files[0]; 286 | 287 | var reader = new FileReader(); 288 | 289 | reader.readAsText(file,'utf8'); 290 | reader.onload = function () { 291 | ipcRenderer.send('sent_dna_fa', this.result) 292 | }; 293 | } 294 | 295 | 296 | function read_cds_fa() { 297 | var inputfile = document.getElementById('cds_file'); 298 | 299 | var file = inputfile.files[0]; 300 | 301 | var reader = new FileReader(); 302 | 303 | reader.readAsText(file,'utf8'); 304 | reader.onload = function () { 305 | ipcRenderer.send('sent_cds_fa', this.result) 306 | }; 307 | } 308 | 309 | 310 | 311 | ipcRenderer.on('append_isoform', function (event, data) { 312 | $('#isoform_num').empty(); 313 | for (var i=1; i<=data; i++ ){ 314 | $("#isoform_num").append("\"\"") 315 | } 316 | }); 317 | 318 | function analyse() { 319 | if ($("#isoform_num").val()){ 320 | form_info.isform = $("#isoform_num").val() 321 | }else {form_info.isform = $("#isoform_num2").val()} 322 | 323 | form_info.pam = $('#PAM').val().toUpperCase(); 324 | form_info.grna_length = Number($('#gRNA_length').val()); 325 | form_info.Edit_window_start = Number($('#Edit_window_start').val()); 326 | form_info.Edit_window_end = Number($('#Edit_window_end').val()); 327 | form_info.dna_sequence = $('#dna_sequence').val().toUpperCase(); 328 | form_info.cds_sequence = $('#cds_sequence').val().toUpperCase(); 329 | if ($("#fasta_content").css("display")==='block'){ 330 | form_info.FA = true 331 | } 332 | if ($('#dna_sequence').val() !== ''){form_info.DS = true} 333 | if ($('#dna_file').val() !== ''){form_info.DF = true} 334 | if ($('#cds_sequence').val() !== ''){form_info.CS = true} 335 | if ($('#cds_file').val() !== ''){form_info.CF = true} 336 | form_info.database = $('#offtarget').val(); 337 | 338 | ipcRenderer.send('analyse', form_info); 339 | ipcRenderer.on('no_hit', function (event, data) { 340 | alert('CDS NO Hit DNA,Please enter again') 341 | }) 342 | } 343 | 344 | ipcRenderer.on('gb_err', function () { 345 | alert("Oops... Please input right format file."); 346 | // $('#gb_file').val("") 347 | }); 348 | 349 | //function change_editor() { 350 | // if ($('#pam').val() === 'TTTV'){$('#grna_length').val('23')} 351 | // if ($('#pam').val() === 'NGG'){$('#grna_length').val('20')} 352 | //} 353 | 354 | function change_Cas9_variants() { 355 | if ($('#Cas9_variants').val() === 'spCas9(NGG)'){$('#PAM').val('NGG')} 356 | if ($('#Cas9_variants').val() === 'spCas9-VQR(NGA)'){$('#PAM').val('NGA')} 357 | if ($('#Cas9_variants').val() === 'spCas9-NG(NG)'){$('#PAM').val('NG')} 358 | if ($('#Cas9_variants').val() === 'spCas9-NRRH(NRRH)'){$('#PAM').val('NRRH')} 359 | if ($('#Cas9_variants').val() === 'spCas9-NRCH(NRCH)'){$('#PAM').val('NRCH')} 360 | if ($('#Cas9_variants').val() === 'spCas9-NRTH(NRTH)'){$('#PAM').val('NRTH')} 361 | if ($('#Cas9_variants').val() === 'SpRYCas9(NRN)'){$('#PAM').val('NRN')} 362 | if ($('#Cas9_variants').val() === 'SpRYcas9(NYN)'){$('#PAM').val('NYN')} 363 | $('#gRNA_length').val('20') 364 | } 365 | 366 | function change_Deaminase() { 367 | if ($('#Deaminase').val() === 'Cas9D10A-PmCDA1-UGI'){$('#Edit_window_start').val('2'),$('#Edit_window_end').val('6')} 368 | if ($('#Deaminase').val() === 'PmCDA1-CBE_V02'){$('#Edit_window_start').val('2'),$('#Edit_window_end').val('6')} 369 | if ($('#Deaminase').val() === 'BE3-hAID'){$('#Edit_window_start').val('4'),$('#Edit_window_end').val('12')} 370 | if ($('#Deaminase').val() === 'BE3-rAPOBEC1'){$('#Edit_window_start').val('4'),$('#Edit_window_end').val('12')} 371 | if ($('#Deaminase').val() === 'BE3-A3A'){$('#Edit_window_start').val('4'),$('#Edit_window_end').val('12')} 372 | if ($('#Deaminase').val() === 'BE3-A3A/Y130F'){$('#Edit_window_start').val('4'),$('#Edit_window_end').val('12')} 373 | if ($('#Deaminase').val() === 'A3A/Y130F-CBE_V02'){$('#Edit_window_start').val('4'),$('#Edit_window_end').val('12')} 374 | } 375 | 376 | 377 | function download_offtarget_info(){ 378 | if($("#download_refresh").css("display")==='none') { 379 | $("#download_refresh").slideToggle("slow"); 380 | } 381 | 382 | let download = wget.download('https://sourceforge.net/projects/crispr-bets/files/' + $('#download').val(), './offtarget_info/'+$('#download').val()); 383 | 384 | download.on('error', function(err) { 385 | console.log(err); 386 | }); 387 | 388 | download.on('start', function(fileSize) { 389 | console.log(fileSize); 390 | if($("#download_finish").css("display")==='inline') { 391 | $("#download_finish").slideToggle("slow"); 392 | } 393 | 394 | if($("#download_check").css("display")==='inline-block') { 395 | $("#download_check").slideToggle("slow"); 396 | } 397 | 398 | $("#file_size").text('Download File Size:' + Math.ceil(fileSize/1000000) + 'Mb') 399 | }); 400 | 401 | download.on('end', function(output) { 402 | console.log(output); 403 | if($("#download_refresh").css("display")==='inline-block') { 404 | $("#download_refresh").slideToggle("slow"); 405 | } 406 | $("#download_finish").slideToggle("slow"); 407 | $("#download_check").slideToggle("slow"); 408 | 409 | // 下载介绍后在offtarget栏添加信息 410 | fs.readdir('./offtarget_info/', function (err, files) { 411 | if (err) {console.log('read file direction failed')} 412 | else { 413 | if (files.indexOf($('#download').val() != -1)){ 414 | $("#offtarget").append("") 415 | } 416 | } 417 | }); 418 | 419 | }); 420 | 421 | download.on('progress', function(progress) { 422 | 423 | $("#download_progress").css("width", parseInt(progress*100) + "%").text(parseInt(progress*100) + "%"); 424 | 425 | }); 426 | 427 | if($("#download_info").css("display")==='none') { 428 | $("#download_info").slideToggle("slow"); 429 | } 430 | 431 | } 432 | 433 | 434 | 435 | function offtarget_file_table(file_name){ 436 | file_table = { 437 | "tigr7_20_NGG_ETScodon_gRNA_m3_offtarget.json":'Oryza sativa japonica(MSU7) NGG offtarget database', 438 | "tigr7_20_NGA_ETScodon_gRNA_m3_offtarget.json":'Oryza sativa japonica(MSU7) NGA offtarget database', 439 | "tigr7_20_NAAR_ETScodon_gRNA_m3_offtarget.json":'Oryza sativa japonica(MSU7) NAAR offtarget database', 440 | "tigr7_20_NGGNG_ETScodon_gRNA_m3_offtarget.json":'Oryza sativa japonica(MSU7) NGGNG offtarget database', 441 | "tigr7_20_NNAGAAW_ETScodon_gRNA_m3_offtarget.json":'Oryza sativa japonica(MSU7) NNAGAAW offtarget database', 442 | "tigr7_20_NNNNGATT_ETScodon_gRNA_m3_offtarget.json":'Oryza sativa japonica(MSU7) NNNNGATT offtarget database', 443 | "tigr7_20_YG_ETScodon_gRNA_m3_offtarget.json":'Oryza sativa japonica(MSU7) YG offtarget database', 444 | 445 | "tair10_20_NGG_ETScodon_gRNA_m3_offtarget.json":'Arabidopsis thaliana(tair10) NGG offtarget database', 446 | "tair10_20_NGA_ETScodon_gRNA_m3_offtarget.json":'Arabidopsis thaliana(tair10) NGA offtarget database', 447 | "tair10_20_NAAR_ETScodon_gRNA_m3_offtarget.json":'Arabidopsis thaliana(tair10) NAAR offtarget database', 448 | "tair10_20_NGGNG_ETScodon_gRNA_m3_offtarget.json":'Arabidopsis thaliana(tair10) NGGNG offtarget database', 449 | "tair10_20_NNAGAAW_ETScodon_gRNA_m3_offtarget.json":'Arabidopsis thaliana(tair10) NNAGAAW offtarget database', 450 | "tair10_20_NNG_ETScodon_gRNA_m3_offtarget.json":'Arabidopsis thaliana(tair10) NNG offtarget database', 451 | "tair10_20_NNNNGATT_ETScodon_gRNA_m3_offtarget.json":'Arabidopsis thaliana(tair10) NNNNGATT offtarget database', 452 | "tair10_20_NR_ETScodon_gRNA_m3_offtarget.json":'Arabidopsis thaliana(tair10) NR offtarget database', 453 | "tair10_20_YG_ETScodon_gRNA_m3_offtarget.json":'Arabidopsis thaliana(tair10) YG offtarget database', 454 | 455 | "RefGen_v4_20_NGG_ETScodon_gRNA_m3_offtarget.json":'Zea mays(RefGen_v4) NGG offtarget database', 456 | "RefGen_v4_20_NGA_ETScodon_gRNA_m3_offtarget.json":'Zea mays(RefGen_v4) NGA offtarget database', 457 | "RefGen_v4_20_NAAR_ETScodon_gRNA_m3_offtarget.json":'Zea mays(RefGen_v4) NAAR offtarget database', 458 | "RefGen_v4_20_NGGNG_ETScodon_gRNA_m3_offtarget.json":'Zea mays(RefGen_v4) NGGNG offtarget database', 459 | "RefGen_v4_20_NNAGAAW_ETScodon_gRNA_m3_offtarget.json":'Zea mays(RefGen_v4) NNAGAAW offtarget database', 460 | "RefGen_v4_20_NNNNGATT_ETScodon_gRNA_m3_offtarget.json":'Zea mays(RefGen_v4) NNNNGATT offtarget database', 461 | } 462 | 463 | return file_table[file_name] 464 | } 465 | -------------------------------------------------------------------------------- /index.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 29 | 30 | 31 | 32 | 33 | 36 | 37 | 38 | 58 | 59 | 60 | 61 | 62 | 63 |
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