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Component Starter","license":"MIT","readme":"![Built With Stencil](https://img.shields.io/badge/-Built%20With%20Stencil-16161d.svg?logo=data%3Aimage%2Fsvg%2Bxml%3Bbase64%2CPD94bWwgdmVyc2lvbj0iMS4wIiBlbmNvZGluZz0idXRmLTgiPz4KPCEtLSBHZW5lcmF0b3I6IEFkb2JlIElsbHVzdHJhdG9yIDE5LjIuMSwgU1ZHIEV4cG9ydCBQbHVnLUluIC4gU1ZHIFZlcnNpb246IDYuMDAgQnVpbGQgMCkgIC0tPgo8c3ZnIHZlcnNpb249IjEuMSIgaWQ9IkxheWVyXzEiIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyIgeG1sbnM6eGxpbms9Imh0dHA6Ly93d3cudzMub3JnLzE5OTkveGxpbmsiIHg9IjBweCIgeT0iMHB4IgoJIHZpZXdCb3g9IjAgMCA1MTIgNTEyIiBzdHlsZT0iZW5hYmxlLWJhY2tncm91bmQ6bmV3IDAgMCA1MTIgNTEyOyIgeG1sOnNwYWNlPSJwcmVzZXJ2ZSI%2BCjxzdHlsZSB0eXBlPSJ0ZXh0L2NzcyI%2BCgkuc3Qwe2ZpbGw6I0ZGRkZGRjt9Cjwvc3R5bGU%2BCjxwYXRoIGNsYXNzPSJzdDAiIGQ9Ik00MjQuNywzNzMuOWMwLDM3LjYtNTUuMSw2OC42LTkyLjcsNjguNkgxODAuNGMtMzcuOSwwLTkyLjctMzAuNy05Mi43LTY4LjZ2LTMuNmgzMzYuOVYzNzMuOXoiLz4KPHBhdGggY2xhc3M9InN0MCIgZD0iTTQyNC43LDI5Mi4xSDE4MC40Yy0zNy42LDAtOTIuNy0zMS05Mi43LTY4LjZ2LTMuNkgzMzJjMzcuNiwwLDkyLjcsMzEsOTIuNyw2OC42VjI5Mi4xeiIvPgo8cGF0aCBjbGFzcz0ic3QwIiBkPSJNNDI0LjcsMTQxLjdIODcuN3YtMy42YzAtMzcuNiw1NC44LTY4LjYsOTIuNy02OC42SDMzMmMzNy45LDAsOTIuNywzMC43LDkyLjcsNjguNlYxNDEuN3oiLz4KPC9zdmc%2BCg%3D%3D&colorA=16161d&style=flat-square)\n\n# Table of sgRNA with radial representation\n\n![example display](https://github.com/sophielem/result_page_crispr/blob/master/docs/exmaple.png)\n\n## Usage\nNeed property to launch integrated components. So need *complete_data* to create the __table-crispr__ component to the left side and *alL_data*, *org_names* and potentially *gene* to create __genomic-card__ component.\n\nIf the *gene* property is given, then the __linear-card__ component is created when the user click on a sector on the sunburst.\n\n#### complete_data\nA list of dictionary object in JSON format. Each dictionary has two keys : sequence and occurences. Occurences contains a list of dictionary object with org and all_ref as keys. all_ref contains a list of dictionary object with ref and coords keys which contains a list of coordinates. Coordinate must match the regex : __[+-]\\\\([0-9]\\*,[0-9]*\\\\)__\n```JSON\n[\n    {\n        \"sequence\": \"AAAACTCAAATGAATTGACGGGG\",\n        \"occurences\": [\n            {\n                \"org\": \"Buchnera aphidicola (Cinara tujafilina) GCF_000217635.1\",\n                \"all_ref\": [\n                    {\n                        \"ref\": \"NC_015662.1\",\n                        \"coords\": [\n                            \"-(195725,195747)\"\n                        ]\n                    }\n                ]\n            },\n            {\n                \"org\": \"Aliivibrio wodanis GCF_000953695.1\",\n                \"all_ref\": [\n                    {\n                        \"ref\": \"NZ_LN554846.1\",\n                        \"coords\": [\n                            \"+(2675080,2675102)\",\n                            \"+(2862314,2862336)\",\n                            \"+(2959996,2960018)\",\n                            \"-(507284,507306)\",\n                            \"-(559657,559679)\",\n                            \"-(661047,661069)\"\n                        ]\n                    },\n                    {\n                        \"ref\": \"NZ_LN554847.1\",\n                        \"coords\": [\n                            \"+(894485,894507)\"\n                        ]\n                    }\n                ]\n            }\n        ]\n    }\n]\n```\n\n#### all_data\nA dictionary of organisms selected in JSON format with their referencesn sgRNA on them and their coordinates which must match the regex : __[+-]\\\\([0-9]\\*,[0-9]*\\\\)__\n\n```JSON\n{\n  \"Buchnera aphidicola (Cinara tujafilina) GCF_000217635.1\":\n  {\"NC_015662.1\":\n    {\"AAAACTCAAATGAATTGACGGGG\":\n      [\"-(195725,195747)\"],\n    \"AAACTCAAATGAATTGACGGGGG\":\n      [\"-(195726,195748)\"],\n    \"TCCCCACTGCTGCCTCCCGTAGG\":\n      [\"+(506719,506741)\", \"+(559092,559114)\", \"+(660482,660504)\", \"-(2675645,2675667)\", \"-(2862879,2862901)\", \"-(2960561,2960583)\"]\n    }\n  },\n  \"Aliivibrio wodanis GCF_000953695.1\":\n    {\"NZ_LN554846.1\":\n      {\"AAAACTCAAATGAATTGACGGGG\":\n        [\"+(2675080,2675102)\", \"+(2862314,2862336)\", \"+(2959996,2960018)\", \"-(507284,507306)\", \"-(559657,559679)\", \"-(661047,661069)\"]\n      },\n    \"NZ_LN554847.1\":\n      {\"AAAACTCAAATGAATTGACGGGG\":\n        [\"+(894485,894507)\"]\n      }\n    }\n}\n```\n\n#### org_names\nA string of organisms names selected seperated by \"&\".\n```\n\"Enterobacter sp. 638 GCF_000016325.1&Candidatus Blochmannia vafer str. BVAF GCF_000185985.2\"\n```\n\n#### size\nIf no precise, all size are set to 4,518,734.\n```JSON\n{\n  \"Enterobacter sp. 638 GCF_000016325.1\":\n    {\"NC_009436.1\":100000},\n  \"Candidatus Blochmannia vafer str. BVAF GCF_000185985.2\":\n    {\"NC_014909.2\": 2000000}}\n```\n\n#### gene\nA dictionary object with organisms as keys and their references. Then, a list of dictionary with *start* and *end* keys to indicate coordinates of gene.\n```JSON\n{\n  \"Enterobacter sp. 638 GCF_000016325.1\":\n    {\"NC_009436.1\":\n      [{\"start\": \"255180\", \"end\": \"255599\"}, {\"start\": \"842680\", \"end\": \"843099\"}, {\"start\": \"3343077\", \"end\": \"3343496\"}, {\"start\": \"4024310\", \"end\": \"4024729\"}, {\"start\": \"4269724\", \"end\": \"4270143\"}, {\"start\": \"4360796\", \"end\": \"4361215\"}, {\"start\": \"4466539\", \"end\": \"4466958\"}]\n    },\n  \"Candidatus Blochmannia vafer str. BVAF GCF_000185985.2\":\n    {\"NC_014909.2\":\n      [{\"start\": \"626246\", \"end\": \"626664\"}]\n    }\n}\n```\n\n\n## Event\n \\*\\*\\*\\*\\* __GENOMIC-CARD__  \\*\\*\\*\\*\\*\n### Emit\n* __changeOrgCard__ : sent the name of the organism selected\n\n* __changeRefCard__ : sent the reference selected\n\n* __changeSgrnaCard__ : sent the sgRNA selected\n\n* __sgDataSection__ : sent : *allSgrna* --> dictionary of sgRNA with their coordinates in a list<br> *gene* --> a list of dictionary containing start and stop for genes\n\n### Send\n* __changeOrgCard__ : change the organism selected, find data associated to this organism and create a new representation\n\n* __changeRefCard__ : change the reference selected, find data associated and create a new representation\n\n* __changeSgrnaCard__ : represent sgRNA selected by a red vertical line around the circle\n\n* __changeOrgRefSgrna__ : find name of the organism name and its reference in *axis* key and sgRNA selected in *sgrna* key. Find data associated and create a new representation\n\n## Authors\nSophie LEMATRE\n\n## Date\nJuly 22 2019\n","readmeFilename":"readme.md","homepage":"https://github.com/MMSB-MOBI/result_page_crispr#readme","repository":{"type":"git","url":"git+https://github.com/MMSB-MOBI/result_page_crispr.git"},"author":{"name":"S.Lematre, C.Hilpert"},"bugs":{"url":"https://github.com/MMSB-MOBI/result_page_crispr/issues"}}