https://github.com/dfornika/amrhike
Proof-of-concept for storing and querying harmonized AMR Genomic Analysis Results in datahike
https://github.com/dfornika/amrhike
antimicrobial-resistance clojure data-harmonization datahike triplestore
Last synced: 2 months ago
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Proof-of-concept for storing and querying harmonized AMR Genomic Analysis Results in datahike
- Host: GitHub
- URL: https://github.com/dfornika/amrhike
- Owner: dfornika
- License: epl-2.0
- Created: 2020-04-02T23:57:00.000Z (about 5 years ago)
- Default Branch: master
- Last Pushed: 2020-04-03T00:05:39.000Z (about 5 years ago)
- Last Synced: 2025-01-24T23:49:11.855Z (4 months ago)
- Topics: antimicrobial-resistance, clojure, data-harmonization, datahike, triplestore
- Language: Clojure
- Homepage:
- Size: 13.7 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
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README
# amrhike
A proof-of-concept for storage and querying of [harmonized Antimicrobial Resistance Genomic Analysis Results](https://github.com/pha4ge/harmonized-amr-parsers)
## Installation
Follow installation instructions for [Leiningen](https://leiningen.org/) for your system
## Usage
```bash
lein run
```
Currently, the program is designed to load a small set of harmonized AMR Genomic Analysis Result
files into a [datahike](https://github.com/replikativ/datahike) database.
It then runs the following query:
```edn
[: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:
```json
[ {
"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.