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agave's Introduction

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

agave's People

Contributors

hannahgooden avatar merritt-brian avatar

Stargazers

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Watchers

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agave's Issues

Improve UX for uploading a file

If a user uploads a file, then switches to one of the built-in files loaded into AGAVE, it is not straightforward to switch back to the uploaded file. Improve the UX for this flow

Support multi organism viewing

  • Change the organism dropdown to be a multi select box
  • Change the heatmap x axes to not include amino acids
  • Add amino acids to the heatmap cells as a single letter of text
  • Change the reference/pdb toggle to be a consensus/reference toggle and use it to switch the letter shown in the cell
  • When a cell is clicked, the molecule viewer should load the molecule for that organism. It should be smart enough not to reload if it's the same
  • Add a toggle that turns the cell text on/off. Turn this off by default if the cells are reduced to a certain size
  • Bonus: group the heatmap rows by organism, and add a visual indicator for organism

Add loading spinners

When a lot of data is loaded, the heatmap takes forever to regenerate. Add a loading spinner that spins until the heatmap is finished redrawing.

Fix square jumping bug

When a heatmap setting is changed, the first cell in the heatmap jumps to a different position. This results in incorrect data being shown.

Fix save svg button

The background of an exported svg is black and does not include the y axis sample labels.

Update PDB Querying

Uniprot Updated their API system, requiring a job submission and polling/querying to get results AFTER the fact. This breaks the uniprot molecule viewer currently

Need to update controllers/vcf_to_json.py

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