README.md

barda

Project setup

npm install

Compiles and hot-reloads for development

npm run serve

Compiles and minifies for production

npm run build

Lints and fixes files

npm run lint

Customize configuration

See Configuration Reference.

Controllers

Running pipelne to get json

SINGLE FILE Use Variant or consensus called depth at positions from vcf file(s), use tsv

python3 controllers/src/vcfs_to_json.py
-i $tsv_iva_file
-o output/out.json
--filetype tsv
-cad ALT_DP
-crd REF_DP
-ct TOTAL_DP
--gb data/proteins/nCoV2.gb
--get_gb
--email "$yourEmail"
--depth $depthFile
--depth_type "variant"

Multiple SAMPLES/FILES Use Variant or consensus called depth at positions from vcf file(s), use tsv

python3 controllers/src/vcfs_to_json.py
-i $ivar_dir
-o output/out.json
--filetype tsv
-cad ALT_DP
-crd REF_DP
-ct TOTAL_DP
--gb data/proteins/nCoV2.gb
--get_gb
--dir
--email "$yourEmail"
--depth $depth_dir
--dir_depth
--depth_type "variant"

Multiple SAMPLES/FILES Use Base Depth for all positions, use tsv

python3 controllers/src/vcfs_to_json.py
-i $ivar_variants_dir
-o output/out.json
--filetype tsv
-cad ALT_DP
-crd REF_DP
-ct TOTAL_DP
--gb data/proteins/nCoV2.gb
--get_gb
--dir
--email "$yourEmail"
--depth $depth_dir
--dir_depth
--depth_type "full"
-map_pdb data/mappings//mapped_pdb.tsv

SINGLE FILE Use Base Depth rather than variant or consensus called depth at positions, use tsv

python3 controllers/src/vcfs_to_json.py
-i $tsv_from_ivar
-o output/out.json
--filetype tsv
-cad ALT_DP
-crd REF_DP
--gb data/proteins/nCoV2.gb
--get_gb
--email "$yourEmail"
--depth $depthFile
--depth_type "full" -map_pdb data/mappings//mapped_pdb.tsv

SINGLE FILE User depth defined in variant call file or consensus output, use vcf files

python3 controllers/src/vcfs_to_json.py
-i $vcf
-o output/out.json
--filetype vcf
--get_gb
--email $email
--depth $depthFile
--depth_type variant
--gb data/proteins/nCoV2.gb
-map_pdb data/mappings//mapped_pdb.tsv

SINGLE FILE Use Base Depth rather than variant or consensus called depth at positions, use vcf files

python3 controllers/src/vcfs_to_json.py
-i $vcf
-o output/out.json
--filetype vcf
-c ALT_DP
--get_gb
--email $email
--depth $depthFile
--depth_type full
--gb data/proteins/nCoV2.gb
-map_pdb data/mappings//mapped_pdb.tsv

SINGLE FILE, MISSING GB FILES Use Base Depth rather than variant or consensus called depth at positions, use vcf files

python3 controllers/src/vcfs_to_json.py
-i $vcf
-o output/out.json
--filetype vcf
-cad ALT_DP
-crd REF_DP \ --get_gb
--email $email
--depth $depthTxtFile
--depth_type full
-map_pdb data/mappings//mapped_pdb.tsv

Convert old json format to newer on (IVA specificially )

python3 controllers/src/vcfs_to_json.py
-i $json1
-o output/out.json
--filetype json --depth_type "variant"
--gb data/proteins/iva_HA_h1n1.gb data/proteins/iva_m1_m2_h1n1.gb data/proteins/iva_NA_h1n1.gb data/proteins/iva_np_h1n1.gb data/proteins/iva_NS1_NEP_h1n1.gb data/proteins/iva_pa_h1n1.gb data/proteins/iva_pb1_h1n1.gb data/proteins/iva_pb2_h1n1.gb
-map_pdb data/mappings//mapped_pdb.tsv

Merge Files (one or more output/out.jsons)

python3 controllers/src/vcfs_to_json.py -i $json1 $json2 -o out.merged.json --merge