Skip to content

Commit

Permalink
feat: AAMutations with multiple sequences
Browse files Browse the repository at this point in the history
  • Loading branch information
Taepper committed Aug 9, 2023
1 parent ce0aba7 commit 80bdc8a
Show file tree
Hide file tree
Showing 5 changed files with 353 additions and 70 deletions.
48 changes: 24 additions & 24 deletions endToEndTests/test/queries/aaMutDistribution.json
Original file line number Diff line number Diff line change
Expand Up @@ -13,122 +13,122 @@
"expectedQueryResult": [
{
"count": 37,
"position": "T19R",
"position": "S:T19R",
"proportion": 0.3854166666666667
},
{
"count": 37,
"position": "G142D",
"position": "S:G142D",
"proportion": 0.49333333333333335
},
{
"count": 34,
"position": "R158G",
"position": "S:R158G",
"proportion": 0.3655913978494624
},
{
"count": 34,
"position": "G339D",
"position": "S:G339D",
"proportion": 0.3469387755102041
},
{
"count": 33,
"position": "S373P",
"position": "S:S373P",
"proportion": 0.3402061855670103
},
{
"count": 33,
"position": "S375F",
"position": "S:S375F",
"proportion": 0.336734693877551
},
{
"count": 38,
"position": "L452R",
"position": "S:L452R",
"proportion": 0.4318181818181818
},
{
"count": 32,
"position": "S477N",
"position": "S:S477N",
"proportion": 0.34408602150537637
},
{
"count": 69,
"position": "T478K",
"position": "S:T478K",
"proportion": 0.7340425531914894
},
{
"count": 31,
"position": "E484A",
"position": "S:E484A",
"proportion": 0.3333333333333333
},
{
"count": 31,
"position": "Q493R",
"position": "S:Q493R",
"proportion": 0.3333333333333333
},
{
"count": 30,
"position": "Q498R",
"position": "S:Q498R",
"proportion": 0.3225806451612903
},
{
"count": 41,
"position": "N501Y",
"position": "S:N501Y",
"proportion": 0.44086021505376344
},
{
"count": 30,
"position": "Y505H",
"position": "S:Y505H",
"proportion": 0.3225806451612903
},
{
"count": 98,
"position": "D614G",
"position": "S:D614G",
"proportion": 0.98989898989899
},
{
"count": 37,
"position": "H655Y",
"position": "S:H655Y",
"proportion": 0.37373737373737376
},
{
"count": 34,
"position": "N679K",
"position": "S:N679K",
"proportion": 0.34
},
{
"count": 42,
"position": "P681H",
"position": "S:P681H",
"proportion": 0.42
},
{
"count": 38,
"position": "P681R",
"position": "S:P681R",
"proportion": 0.38
},
{
"count": 31,
"position": "N764K",
"position": "S:N764K",
"proportion": 0.32978723404255317
},
{
"count": 34,
"position": "D796Y",
"position": "S:D796Y",
"proportion": 0.3469387755102041
},
{
"count": 34,
"position": "D950N",
"position": "S:D950N",
"proportion": 0.35789473684210527
},
{
"count": 33,
"position": "Q954H",
"position": "S:Q954H",
"proportion": 0.34375
},
{
"count": 34,
"position": "N969K",
"position": "S:N969K",
"proportion": 0.35051546391752575
}
]
Expand Down
64 changes: 64 additions & 0 deletions endToEndTests/test/queries/aaMutDistribution_all.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,64 @@
{
"testCaseName": "The distribution of Amino Acid Mutations action for all sequences",
"query": {
"action": {
"type": "AminoAcidMutations",
"minProportion": 0.4
},
"filterExpression": {
"type": "True"
}
},
"expectedQueryResult": [
{
"count": 46,
"position": "N:R203K",
"proportion": 0.46
},
{
"count": 46,
"position": "N:G204R",
"proportion": 0.46
},
{
"count": 64,
"position": "ORF1a:T3255I",
"proportion": 0.6464646464646465
},
{
"count": 98,
"position": "ORF1b:P314L",
"proportion": 0.98989898989899
},
{
"count": 37,
"position": "S:G142D",
"proportion": 0.49333333333333335
},
{
"count": 38,
"position": "S:L452R",
"proportion": 0.4318181818181818
},
{
"count": 69,
"position": "S:T478K",
"proportion": 0.7340425531914894
},
{
"count": 41,
"position": "S:N501Y",
"proportion": 0.44086021505376344
},
{
"count": 98,
"position": "S:D614G",
"proportion": 0.98989898989899
},
{
"count": 42,
"position": "S:P681H",
"proportion": 0.42
}
]
}
170 changes: 170 additions & 0 deletions endToEndTests/test/queries/aaMutDistribution_multiple.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,170 @@
{
"testCaseName": "The distribution of Amino Acid Mutations action for multiple sequences",
"query": {
"action": {
"type": "AminoAcidMutations",
"sequenceName": ["S", "N"],
"minProportion": 0.3
},
"filterExpression": {
"type": "True"
}
},
"expectedQueryResult": [
{
"count": 37,
"position": "S:T19R",
"proportion": 0.3854166666666667
},
{
"count": 37,
"position": "S:G142D",
"proportion": 0.49333333333333335
},
{
"count": 34,
"position": "S:R158G",
"proportion": 0.3655913978494624
},
{
"count": 34,
"position": "S:G339D",
"proportion": 0.3469387755102041
},
{
"count": 33,
"position": "S:S373P",
"proportion": 0.3402061855670103
},
{
"count": 33,
"position": "S:S375F",
"proportion": 0.336734693877551
},
{
"count": 38,
"position": "S:L452R",
"proportion": 0.4318181818181818
},
{
"count": 32,
"position": "S:S477N",
"proportion": 0.34408602150537637
},
{
"count": 69,
"position": "S:T478K",
"proportion": 0.7340425531914894
},
{
"count": 31,
"position": "S:E484A",
"proportion": 0.3333333333333333
},
{
"count": 31,
"position": "S:Q493R",
"proportion": 0.3333333333333333
},
{
"count": 30,
"position": "S:Q498R",
"proportion": 0.3225806451612903
},
{
"count": 41,
"position": "S:N501Y",
"proportion": 0.44086021505376344
},
{
"count": 30,
"position": "S:Y505H",
"proportion": 0.3225806451612903
},
{
"count": 98,
"position": "S:D614G",
"proportion": 0.98989898989899
},
{
"count": 37,
"position": "S:H655Y",
"proportion": 0.37373737373737376
},
{
"count": 34,
"position": "S:N679K",
"proportion": 0.34
},
{
"count": 42,
"position": "S:P681H",
"proportion": 0.42
},
{
"count": 38,
"position": "S:P681R",
"proportion": 0.38
},
{
"count": 31,
"position": "S:N764K",
"proportion": 0.32978723404255317
},
{
"count": 34,
"position": "S:D796Y",
"proportion": 0.3469387755102041
},
{
"count": 34,
"position": "S:D950N",
"proportion": 0.35789473684210527
},
{
"count": 33,
"position": "S:Q954H",
"proportion": 0.34375
},
{
"count": 34,
"position": "S:N969K",
"proportion": 0.35051546391752575
},
{
"count": 34,
"position": "N:P13L",
"proportion": 0.3469387755102041
},
{
"count": 36,
"position": "N:D63G",
"proportion": 0.3673469387755102
},
{
"count": 46,
"position": "N:R203K",
"proportion": 0.46
},
{
"count": 38,
"position": "N:R203M",
"proportion": 0.38
},
{
"count": 46,
"position": "N:G204R",
"proportion": 0.46
},
{
"count": 30,
"position": "N:G215C",
"proportion": 0.3
},
{
"count": 37,
"position": "N:D377Y",
"proportion": 0.38144329896907214
}
]
}
Loading

0 comments on commit 80bdc8a

Please sign in to comment.