ngs2fhir is a tool to convert the Next generation sequencing (NGS) data to the FHIR Resources
npm install
- inputPath：NGS annotation file, support csv or xlsx
- outPath：Save path of converted result
- moudule：NGS annotation file format
# 1. Chromosome
$ mkdir -p ./csv2fhir/GenomeReference/FHIR
$ curl https://www.hl7.org/fhir/codesystem-chromosome-human.json > ./csv2fhir/GenomeReference/FHIR/codesystem-chromosome-
# 2. Human Genome
$ mkdir -p ./models/csv2fhir/GenomeReference/hg19
$ mkdir -p ./models/csv2fhir/GenomeReference/hg38
$ curl https://hgdownload.soe.ucsc.edu/goldenPath/hg19/chromosomes/chr*.fa.gz > ./models/csv2fhir/GenomeReference/hg19/chr*.fa.gz
$ curl https://hgdownload.soe.ucsc.edu/goldenPath/hg19/chromosomes/chr*.fa.gz > ./models/csv2fhir/GenomeReference/hg19/chr*.fa.gz
$ gunzip ./models/csv2fhir/GenomeReference/hg19/chr*.fa.gz
# 3. HGNC
$ mkdir -p ./models/csv2fhir/GenomeReference/HGNC
$ curl http:https://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/json/hgnc_complete_set.json > ./models/csv2fhir/GenomeReference/HGNC/hgnc_complete_set.json
# 4. LOINC
$ mkdir -p ./models/csv2fhir/GenomeReference/LOINC
(next step below)- Path：https://loinc.org/file-access/download-id/8809
- Use csv2json tool convert "/LoincTableCore/LoincTableCore.csv" to "LoincTableCore.json"
- Use csv2json tool convert "/AccessoryFiles/AnswerFile/AnswerList.csv" to "AnswerList.json"
$ vi ./models/csv2fhir/tools/csv2json.js # Edit Filename and Path
$ node ./csv2fhir/tools/csv2json.js
$ mv LoincTableCore.json ./csv2fhir/GenomeReference/LOINC/$ vi ./models/csv2fhir/tools/fa_tool.js # Edit Filenmae and Path
$ node ./csv2fhir/tools/fa_tool.js # Repeat for all .fa files- Edit "
setting" in your need npm start