amrhike

A proof-of-concept for storage and querying of harmonized Antimicrobial Resistance Genomic Analysis Results

Installation

Follow installation instructions for Leiningen for your system

Usage

lein run

Currently, the program is designed to load a small set of harmonized AMR Genomic Analysis Result files into a datahike database.

It then runs the following query:

[:find
 ?sample ?tool ?gene ?contig ?start ?stop
 :where [?e :gene_symbol "catA1"]
        [?e :gene_symbol ?gene]
        [?e :sample_id ?sample]
        [?e :analysis_software_name ?tool]
        [?e :contig_id ?contig]
        [?e :start ?start]
        [?e :stop ?stop]]

...which essentially means "find all results where the catA1 gene was found, and display a subset of fields associated with those results"

The result is printed in JSON format to standard output, and should look like:

[ {
  "sample_id" : "SAMEA6058467",
  "analysis_software_name" : "AMRFinderPlus",
  "gene_symbol" : "catA1",
  "contig_id" : "DAAGAT010000085.1",
  "start" : 43,
  "stop" : 699
}, {
  "sample_id" : "SAMEA6058467",
  "analysis_software_name" : "AMRFinderPlus",
  "gene_symbol" : "catA1",
  "contig_id" : "DAAGAT010000041.1",
  "start" : 222,
  "stop" : 878
}, {
  "sample_id" : "SAMEA6058467",
  "analysis_software_name" : "ABRicate",
  "gene_symbol" : "catA1",
  "contig_id" : "DAAGAT010000041.1",
  "start" : 222,
  "stop" : 881
}, {
  "sample_id" : "SAMEA6058467",
  "analysis_software_name" : "ABRicate",
  "gene_symbol" : "catA1",
  "contig_id" : "DAAGAT010000085.1",
  "start" : 43,
  "stop" : 702
} ]

License

Copyright © 2020 Dan Fornika

This program and the accompanying materials are made available under the terms of the Eclipse Public License 2.0 which is available at http://www.eclipse.org/legal/epl-2.0.

This Source Code may also be made available under the following Secondary Licenses when the conditions for such availability set forth in the Eclipse Public License, v. 2.0 are satisfied: GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version, with the GNU Classpath Exception which is available at https://www.gnu.org/software/classpath/license.html.