{"id":16873773,"url":"https://github.com/dfornika/amrhike","last_synced_at":"2025-10-14T13:05:50.135Z","repository":{"id":149830791,"uuid":"252590885","full_name":"dfornika/amrhike","owner":"dfornika","description":"Proof-of-concept for storing and querying harmonized AMR Genomic Analysis Results in 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amrhike\n\nA proof-of-concept for storage and querying of [harmonized Antimicrobial Resistance Genomic Analysis Results](https://github.com/pha4ge/harmonized-amr-parsers)\n\n## Installation\n\nFollow installation instructions for [Leiningen](https://leiningen.org/) for your system\n\n## Usage\n\n```bash\nlein run\n```\n\nCurrently, the program is designed to load a small set of harmonized AMR Genomic Analysis Result\nfiles into a [datahike](https://github.com/replikativ/datahike) database.\n\nIt then runs the following query:\n\n```edn\n[:find\n ?sample ?tool ?gene ?contig ?start ?stop\n :where [?e :gene_symbol \"catA1\"]\n        [?e :gene_symbol ?gene]\n        [?e :sample_id ?sample]\n        [?e :analysis_software_name ?tool]\n        [?e :contig_id ?contig]\n        [?e :start ?start]\n        [?e :stop ?stop]]\n```\n\n...which essentially means \"find all results where the `catA1` gene was found, and display a subset of fields associated with those results\"\n\nThe result is printed in JSON format to standard output, and should look like:\n\n```json\n[ {\n  \"sample_id\" : \"SAMEA6058467\",\n  \"analysis_software_name\" : \"AMRFinderPlus\",\n  \"gene_symbol\" : \"catA1\",\n  \"contig_id\" : \"DAAGAT010000085.1\",\n  \"start\" : 43,\n  \"stop\" : 699\n}, {\n  \"sample_id\" : \"SAMEA6058467\",\n  \"analysis_software_name\" : \"AMRFinderPlus\",\n  \"gene_symbol\" : \"catA1\",\n  \"contig_id\" : \"DAAGAT010000041.1\",\n  \"start\" : 222,\n  \"stop\" : 878\n}, {\n  \"sample_id\" : \"SAMEA6058467\",\n  \"analysis_software_name\" : \"ABRicate\",\n  \"gene_symbol\" : \"catA1\",\n  \"contig_id\" : \"DAAGAT010000041.1\",\n  \"start\" : 222,\n  \"stop\" : 881\n}, {\n  \"sample_id\" : \"SAMEA6058467\",\n  \"analysis_software_name\" : \"ABRicate\",\n  \"gene_symbol\" : \"catA1\",\n  \"contig_id\" : \"DAAGAT010000085.1\",\n  \"start\" : 43,\n  \"stop\" : 702\n} ]\n```\n\n## License\n\nCopyright © 2020 Dan Fornika\n\nThis program and the accompanying materials are made available under the\nterms of the Eclipse Public License 2.0 which is available at\nhttp://www.eclipse.org/legal/epl-2.0.\n\nThis Source Code may also be made available under the following Secondary\nLicenses when the conditions for such availability set forth in the Eclipse\nPublic License, v. 2.0 are satisfied: GNU General Public License as published by\nthe Free Software Foundation, either version 2 of the License, or (at your\noption) any later version, with the GNU Classpath Exception which is available\nat https://www.gnu.org/software/classpath/license.html.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdfornika%2Famrhike","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdfornika%2Famrhike","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdfornika%2Famrhike/lists"}