{"id":20387007,"url":"https://github.com/cmdcolin/region_retriever","last_synced_at":"2026-05-31T22:31:43.436Z","repository":{"id":137213378,"uuid":"198862656","full_name":"cmdcolin/region_retriever","owner":"cmdcolin","description":"A small script to retrieve jbrowse data from a 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jbrowse_region_retriever\n\nA small script to download NCList data from a list of regions\n\n\n## Setup\n\nJust run\n\n```\nnpm install\n```\n\nOr\n\n```\nyarn\n```\n\nTo install the dependencies\n\n## Usage\n\nMake a file called regions.json like this\n\n\nregions.json\n```\n[\n    {\"refName\": \"chr1\", \"start\": 0, \"end\": 10000},\n    {\"refName\": \"chr2\", \"start\": 50000, \"end\": 60000},\n    ...\n]\n```\n\nThen run the script like this\n\nsample usage\n\n    node index.js /path/to/data/directory regions.json\n\nWhere /path/to/data/directory contains a trackList.json\n\n\n## Example output\n\n```\nExampleFeatures\tctgA\t999\t2000\t.\tRemark:hga\nExampleFeatures\tctgA\t1658\t1984\t.\tf07\nExampleFeatures\tctgA\t3013\t6130\t.\tf06\nExampleFeatures\tctgA\t4714\t5968\t.\tf05\nNameTest\tctgA\t1099\t2000\t.\tGene:hga\nNameTest\tctgA\t1199\t1900\t.\tProtein:HGA\nNameTest\tctgA\t1599\t3000\t.\tGene:hgb\nNameTest\tctgA\t1799\t2900\t.\tProtein:HGB\nGenes\tctgA\t1049\t9000\tEDEN\tEDEN\nsnps\tctgA\t999\t1000\tFakeSNP1\tFakeSNP\nReadingFrame\tctgA\t1049\t9000\tEDEN.2\tEDEN.2\nReadingFrame\tctgA\t1049\t9000\tEDEN.1\tEDEN.1\nReadingFrame\tctgA\t1299\t9000\tEDEN.3\tEDEN.3\nClones\tctgA\t999\t20000\tb101.2\tb101.2\nCDS\tctgA\t9999\t11500\t.\tApple1\nEST\tctgA\t1049\t7300\tMatch3\tagt221.5\nEST\tctgA\t1049\t3202\tMatch1\tagt830.5\nEST\tctgA\t1149\t7200\tMatch5\tagt767.5\nEST\tctgA\t5409\t7503\tMatch2\tagt830.3\nEST\tctgA\t7499\t8000\tMatch4\tagt221.3\nEST\tctgA\t7999\t9000\tMatch6\tagt767.3\nChromHMM\tctgA\t0\t11960\t.\t15_Quies\nmalformed_alignments\tctgA\t5232\t5302\t.\tseg04\nmalformed_alignments\tctgA\t5799\t6101\t.\tseg04\nmalformed_alignments\tctgA\t6441\t6854\t.\tseg04\nmalformed_alignments\tctgA\t6884\t7241\t.\tseg03\nmalformed_alignments\tctgA\t7105\t7211\t.\tseg04\nmalformed_alignments\tctgA\t7409\t7737\t.\tseg03\nmalformed_alignments\tctgA\t7694\t8177\t.\tseg04\nmalformed_alignments\tctgA\t8054\t8080\t.\tseg03\nmalformed_alignments\tctgA\t8305\t8999\t.\tseg03\nmalformed_alignments\tctgA\t8544\t8783\t.\tseg04\nmalformed_alignments\tctgA\t8868\t8935\t.\tseg04\nmalformed_alignments\tctgA\t9403\t9825\t.\tseg04\n```\n\nDescription of output\n\n    column 1 - trackLabel\n    column 2 - refName\n    column 3 - start\n    column 4 - end\n    column 5 - feature id or '.' if not exists\n    column 6 - feature name or '.' if not exists\n\nCan customize the output as needed by editing the script\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcmdcolin%2Fregion_retriever","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcmdcolin%2Fregion_retriever","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcmdcolin%2Fregion_retriever/lists"}