Mutation annotations

[ArtPoon]

@nodrogluap is maintaining a site: https://people.ucalgary.ca/~gordonp/S-monoclonal_antibody_serial_passage_escape.html tracking the literature on phenotypic characterization of SARS-CoV-2 mutations - I'm wondering if it would be possible to call out to that site API to annotate lineage mutations so that ones with known significance are highlighted in the tooltip.

[ArtPoon]

@nodrogluap suggests using this Perl script: https://github.com/nodrogluap/pokay/blob/master/text2ui to generate a JSON file from the database, which we can then transfer to client for pre-processing of lineage information.

[Abayomi-Olabode]

I ran the text2ui perl script and here's what the JSON output looks like.

[
  {
    "description": "gene_expression_increase",
    "url": "http://people.ucalgary.ca/~gordonp/S:V483K.html#gene_expression_increase",
    "substitutions": 
      [
        { "refAA": "V", "queryAA": "K", "codon": 483, "gene": "S" }
      ],
    "deletions": 
      [

      ]
  }
,
  {
    "description": "monoclonal_antibody_serial_passage_escape",
    "url": "http://people.ucalgary.ca/~gordonp/S:V483K.html#monoclonal_antibody_serial_passage_escape",
    "substitutions": 
      [
        { "refAA": "V", "queryAA": "K", "codon": 483, "gene": "S" }
      ],
    "deletions": 
      [

      ]
  }
,
  {
    "description": "gene_expression_increase",
    "url": "http://people.ucalgary.ca/~gordonp/S:V503E.html#gene_expression_increase",
    "substitutions": 
      [
        { "refAA": "V", "queryAA": "E", "codon": 503, "gene": "S" }
      ],
    "deletions": 
      [

      ]
  }
,
  {
    "description": "gene_expression_increase",
    "url": "http://people.ucalgary.ca/~gordonp/S:P384K.html#gene_expression_increase",
    "substitutions": 
      [
        { "refAA": "P", "queryAA": "K", "codon": 384, "gene": "S" }
      ],
    "deletions": 
      [

      ]
  }
,
  {
    "description": "monoclonal_antibody_serial_passage_escape",
    "url": "http://people.ucalgary.ca/~gordonp/S:P384K.html#monoclonal_antibody_serial_passage_escape",
    "substitutions": 
      [
        { "refAA": "P", "queryAA": "K", "codon": 384, "gene": "S" }
      ],
    "deletions": 
      [

      ]
  }

[ArtPoon]

Integrate Perl script into pipeline, add acknowledgements

[ArtPoon]

• write script to convert this JSON into a more compact and accessible format (e.g., keyed by mutations in our format, aa:S:D614G)
• distribute this JSON to devs
• parse JSON in front-end and use to (1) modify lineage tooltips, (2) generate new details table (mutations, #310)

[Abayomi-Olabode]

Ran the text2ui perl script as follows;

perl text2ui VOCs.tab data/ html/ mutation_annotations.json

• VOCs.tab => list of lineage_mutations for creating html files (constellations of interest)
• data/ => input directory with phenotypic data files
• html/ => output directory for html files
• mutation_annotations.json => json file containing mutation annotations and functional attributes

[Abayomi-Olabode]

"aa:S:P9S": "monoclonal_antibody_serial_passage_escape"

[Abayomi-Olabode]

1. Clone the pokay repo @ https://github.com/nodrogluap/pokay
2. Run the following command using Perl:

   
   perl text2ui VOCs.tab data/ html/ mutation_annotations.json

• text2ui => perl script written by Paul
• VOCs.tab => list of lineage_mutations for creating html files (constellations of interest)
• data/ => input directory with phenotypic data files
• html/ => output directory for html files (You have to create this directory)
• mutation_annotations.json => json output file containing mutation annotations and functional attributes

  
  3. Run the python script below, to change mutation annotations to our preferred format:

#import python libraries
import json
import re

#define path to working directory
path = "./" # path to cloned pokay directory

# create function to reformat charaterized mutations
# new format => aa, gene, refAA, codon, queryAA
def reformatMutations(subt, dels, func):

    # define list & dictionary object
    # to store data
    mut_list = []
    mut_dict = {}

    # iterate through mutations
    for c, i in enumerate(subt):
        subs = i.values()
        muts = "{}:{}:{}{}{}".format("aa",subs[2], subs[0], subs[3], subs[1])
        mut_list.append(muts)

    # iterate through deletions if any
    for n, j in enumerate(dels):
        if dels == "None":
            dells = []
        else:
            dell = j.values()
            dells = "{}:{}:{}{}{}".format("aa", dell[1], dell[0], dell[2], "-")
            mut_list.append(dells)

    mut_dict[func] = mut_list
    return mut_dict

# open JSON file
# return JSON object as a dictionary
jfile = open(path + 'mutation_annotations.json',)
data = json.load(jfile)

# output JSON
outfile = open(path + 'mut_annotations.json', 'w')

# iterating through pokay generated mutation annotations
for i in range(0, len(data)):
    subs = data[i]["substitutions"]
    dels = data[i]["deletions"]
    func = data[i]["description"]

    #run function
    result = reformatMutations(subs, dels, func)

    # write result to JSON file
    json.dump(result, outfile, indent=4, ensure_ascii=False, separators=(',', ':'))

# closing files
jfile.close()
outfile.close()

# fix JSON file issues, add commas
# and a square brackets at the begin and end of file
with open(path + "mut_annotations.json", "r+") as fyl:
    edit_f = fyl.read()
    fyl.seek(0)
    j_son = '[' + edit_f  + ']'
    j_son = j_son.replace('}{', '},{')
    fyl.write(j_son)
    fyl.close