{"id":15893437,"url":"https://github.com/multimeric/vep-cache-extractor","last_synced_at":"2025-04-02T17:42:56.544Z","repository":{"id":85377406,"uuid":"65522345","full_name":"multimeric/vep-cache-extractor","owner":"multimeric","description":"Command line application to analyse the VEP cache and extract information from each transcript","archived":false,"fork":false,"pushed_at":"2016-11-24T05:09:05.000Z","size":69,"stargazers_count":0,"open_issues_count":0,"forks_count":1,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-03-21T05:23:38.615Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Perl","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/multimeric.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2016-08-12T04:07:08.000Z","updated_at":"2016-11-23T14:46:53.000Z","dependencies_parsed_at":"2023-03-08T13:30:45.308Z","dependency_job_id":null,"html_url":"https://github.com/multimeric/vep-cache-extractor","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/multimeric%2Fvep-cache-extractor","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/multimeric%2Fvep-cache-extractor/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/multimeric%2Fvep-cache-extractor/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/multimeric%2Fvep-cache-extractor/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/multimeric","download_url":"https://codeload.github.com/multimeric/vep-cache-extractor/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":246863828,"owners_count":20846319,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-10-06T08:10:36.602Z","updated_at":"2025-04-02T17:42:56.524Z","avatar_url":"https://github.com/multimeric.png","language":"Perl","funding_links":[],"categories":[],"sub_categories":[],"readme":"# VEP Cache Extractor\n## Introduction\nThe VEP cache extractor is a command line utility for extracting fields from the\ncache used by Ensembl's VEP, or [Variant Effect Predictor](http://asia.ensembl.org/info/docs/tools/vep/index.html)\ntool. The cache itself is a large collection of Perl storable files, each\ncontaining a large list of transcript entries.\n\n## Installation\n\nFirstly, the script requires a modern version of Perl 5 to run. However you probably have such a version if you are running VEP, so this is likely not an issue\n\nTo install the script's dependencies, make sure cpanm is installed with\n```bash\ncpan App::cpanminus\n```\nand then install the dependencies using\n```bash\ncpanm --installdeps .\n```\nIf you are using a system version of Perl, running these commands may give you an error message\nalong these lines: \n```\nCan't write to /usr/local/share/perl/5.22.2 and /usr/local/bin\n```\nIf this is the case, make sure to run these commands with `sudo`\n\nYou'll also need a copy of the VEP cache itself. You may already have one if you're already using VEP. In this case,\nsimply use the directory of the cache as the first argument to the extract script. If not, you can use the downloader script to obtain it,\nand use `vep_cache` (a relative path) as the cache path\n(documented below).\n\n## Downloader Script\nThis script downloads a certain version of the VEP cache into the repository\ndirectory (the same directory as the script). Use it as follows:\n\n```\nUsage: download.sh -c cache_type -e ensembl_release -g genome-build\n  -c, --cache-type\n    The version of the cache to download. Either 'merged', 'ensembl' or 'refseq'\n  -e, --ensembl-release\n    The ensembl release number to download the cache for. e.g. 75, 85 etc.\n  -g, --genome-build\n    The grch build version to download for. e.g. 37, 38\n```\n\n## Usage\nUse the extract script as follows:\n```bash\n./extract.pl /path/to/cache path_1:column_1 path_2:column_2\n```\nIn other words, the script's first argument is a directory path indicating where\nthe cache is located.\n\nThe second and all following arguments are descriptors indicating which field you\nwant to extract from the cache and what to name them. Each argument is a pair of\npath:column_name pairs. For example, this second argument might be `_trans_exon_array.0.stable_id:exon_id` (explained below)\n\n* `path`: A dot separated string, where each segment is a hash key, indicating\nwhich field to choose. For example, `\"_trans_exon_array.0.stable_id\"` would choose the stable_id of the first exon\nin the transcript, which in json terms means extract `transcript[\"_trans_exon_array\"][0][stable_id]` for each transcript.\nYou might find it helpful to look at the sample.json file in the repository, as this will give you some indication as to which fields are stored in the VEP cache.\n* `column_name`: A string indicating the name of the column to store this data in.\nFor example, if we used the path above, along with the column_name of \"exon_id\",\nwe would get output as follows:\n```\nexon_id\n\"id67641\"\n\"id67642\"\n\"NM_152663.3.1\"\n\"XM_005245297.1.1\"\n\"id67643\"\n\"id67663\"\n\"ENSESTE00000219503\"\n\"ENSESTE00000220088\"\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmultimeric%2Fvep-cache-extractor","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmultimeric%2Fvep-cache-extractor","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmultimeric%2Fvep-cache-extractor/lists"}