tests/testthat/test-parse-pairs-max.R
In UW-GAC/wgsaparsr: A R package for Parsing Annotation File for Database Import
context("test_.parse_pairs_max() - unit tests")
test_that(".parse_pairs_max() gives error if pair_columns is not a list", {
example <- tibble::tibble(
Eigen_PC_raw = c(".{1}", "-0.164398825586883{1}",
".{5}-0.00506108216253831{4}0.0200792355286427{1}",
".{5}0.636779480039485{1}0.651616016738356{2}", ".{5}",
".{3}0.382030178748437{1}0.394216023865136{1}",
".{3}-0.0842385276257326{1}-0.0880785370562746{1}",
".;-0.0842385276257326;-0.0880785370562746{1}"
),
fathmm_MKL_coding_score = c(".{1}", "0.87811{1}", ".{5}0.90605{5}",
".{5}0.90734{3}", ".{5}", ".{3}0.90912{2}",
".{3}0.90863{2}", "0.90863{3};0.90863{2}"),
MAP20_149bp = c("0.0{1}", "0.004166664{1}", "0.015773803{10}",
"0.01666666{8}",
"0.09196428{1}0.09553571{1}0.09732143{1}0.09910714{1}",
"0.11339285{1}0.12053571{1}0.12410714{1}0.12767857{1}",
"0.19464286{1}0.19821429{1}0.20178571{1}0.20535715{1}",
"0.19464286{1};0.19821429{1}0.20178571{1};0.20535715{1}")
)
expect_error(.parse_pairs_max(example, "not a list"),
"pair_columns must be a list")
})
test_that(".parse_pairs_max() gives error when parsing a tripple", {
example <- tibble::tibble(
Eigen_PC_raw = c(".{1}", "-0.164398825586883{1}",
".{5}-0.00506108216253831{4}0.0200792355286427{1}",
".{5}0.636779480039485{1}0.651616016738356{2}", ".{5}",
".{3}0.382030178748437{1}0.394216023865136{1}",
".{3}-0.0842385276257326{1}-0.0880785370562746{1}",
".;-0.0842385276257326;-0.0880785370562746{1}"
),
"fathmm_MKL_coding_score" = c(".{1}", "0.87811{1}", ".{5}0.90605{5}",
".{5}0.90734{3}", ".{5}", ".{3}0.90912{2}",
".{3}0.90863{2}", "0.90863{3};0.90863{2}"),
MAP20_149bp = c("0.0{1}", "0.004166664{1}", "0.015773803{10}",
"0.01666666{8}",
"0.09196428{1}0.09553571{1}0.09732143{1}0.09910714{1}",
"0.11339285{1}0.12053571{1}0.12410714{1}0.12767857{1}",
"0.19464286{1}0.19821429{1}0.20178571{1}0.20535715{1}",
"0.19464286{1};0.19821429{1}0.20178571{1};0.20535715{1}")
)
expect_error(.parse_pairs_max(example, list(c("Eigen_PC_raw",
"MAP20_149bp",
"fathmm_MKL_coding_score"))),
"pair columns not length 1 or 2")
})
test_that(".parse_pairs_max() returns expected tibble when parsing a single", {
example <- tibble::tibble(
Eigen_PC_raw = c(".{1}", "-0.164398825586883{1}",
".{5}-0.00506108216253831{4}0.0200792355286427{1}",
".{5}0.636779480039485{1}0.651616016738356{2}", ".{5}",
".{3}0.382030178748437{1}0.394216023865136{1}",
".{3}-0.0842385276257326{1}-0.0880785370562746{1}",
".;-0.0842385276257326;-0.0880785370562746{1}"
),
fathmm_MKL_coding_score = c(".{1}", "0.87811{1}", ".{5}0.90605{5}",
".{5}0.90734{3}", ".{5}", ".{3}0.90912{2}",
".{3}0.90863{2}", "0.90863{3};0.90863{2}"),
MAP20_149bp = c("0.0{1}", "0.004166664{1}", "0.015773803{10}",
"0.01666666{8}",
"0.09196428{1}0.09553571{1}0.09732143{1}0.09910714{1}",
"0.11339285{1}0.12053571{1}0.12410714{1}0.12767857{1}",
"0.19464286{1}0.19821429{1}0.20178571{1}0.20535715{1}",
"0.19464286{1};0.19821429{1}0.20178571{1};0.20535715{1}")
)
target <- tibble::tibble(
Eigen_PC_raw = c(".{1}", "-0.164398825586883{1}",
".{5}-0.00506108216253831{4}0.0200792355286427{1}",
".{5}0.636779480039485{1}0.651616016738356{2}", ".{5}",
".{3}0.382030178748437{1}0.394216023865136{1}",
".{3}-0.0842385276257326{1}-0.0880785370562746{1}",
".;-0.0842385276257326;-0.0880785370562746{1}"
),
fathmm_MKL_coding_score = c(".{1}", "0.87811{1}", ".{5}0.90605{5}",
".{5}0.90734{3}", ".{5}", ".{3}0.90912{2}",
".{3}0.90863{2}", "0.90863{3};0.90863{2}"),
# note: first value of parsed MAP20_149bp is "0", not "0.0". I think that's
# okay
MAP20_149bp = c("0", "0.004166664", "0.015773803", "0.01666666",
"0.09910714", "0.12767857", "0.20535715", "0.20535715"),
MAP20_149bp_unparsed = c("0.0{1}", "0.004166664{1}", "0.015773803{10}",
"0.01666666{8}",
"0.09196428{1}0.09553571{1}0.09732143{1}0.09910714{1}",
"0.11339285{1}0.12053571{1}0.12410714{1}0.12767857{1}",
"0.19464286{1}0.19821429{1}0.20178571{1}0.20535715{1}",
"0.19464286{1};0.19821429{1}0.20178571{1};0.20535715{1}")
)
result <- .parse_pairs_max(example, list(c("MAP20_149bp")))
expect_identical(result, target)
})
test_that(".parse_pairs_max() returns expected tibble when parsing a pair", {
example <- dplyr::tribble(
~Polyphen2_HDIV_score, ~Polyphen2_HDIV_pred, ~Polyphen2_HVAR_score,
~Polyphen2_HVAR_pred,
"0.941;0.941;0.146", "P;P;B", "0.688;0.688;0.138", "P;P;B",
"1.0;1.0;0.999", "D", "0.993;0.993;0.989", "D",
"0.325;0.325;0.243", "B", "0.21;0.21;0.136", "B",
"0.999;0.999;0.994", "D", "0.939;0.939;0.863", "D;D;P",
"0.96;0.96;0.931", "D;D;P", "0.814;0.814;0.699", "P"
)
target <- tibble::tibble(
Polyphen2_HDIV_score_unparsed =
c("0.941;0.941;0.146", "1.0;1.0;0.999", "0.325;0.325;0.243",
"0.999;0.999;0.994", "0.96;0.96;0.931"),
Polyphen2_HDIV_pred_unparsed =
c("P;P;B", "D", "B", "D", "D;D;P"),
Polyphen2_HVAR_score =
c("0.688;0.688;0.138", "0.993;0.993;0.989", "0.21;0.21;0.136",
"0.939;0.939;0.863", "0.814;0.814;0.699"),
Polyphen2_HVAR_pred =
c("P;P;B", "D", "B", "D;D;P", "P"),
Polyphen2_HDIV_score =
c("0.941", "1", "0.325", "0.999", "0.96"),
Polyphen2_HDIV_pred =
c("P", "D", "B", "D", "D")
)
result <- .parse_pairs_max(example,
list(c("Polyphen2_HDIV_score",
"Polyphen2_HDIV_pred")))
expect_identical(result, target)
})
test_that(".parse_pairs_max() returns expected tibble when parsing two pairs", {
example <- dplyr::tribble(
~Polyphen2_HDIV_score, ~Polyphen2_HDIV_pred, ~Polyphen2_HVAR_score,
~Polyphen2_HVAR_pred,
"0.941;0.941;0.146", "P;P;B", "0.688;0.688;0.138", "P;P;B",
"1.0;1.0;0.999", "D", "0.993;0.993;0.989", "D",
"0.325;0.325;0.243", "B", "0.21;0.21;0.136", "B",
"0.999;0.999;0.994", "D", "0.939;0.939;0.863", "D;D;P",
"0.96;0.96;0.931", "D;D;P", "0.814;0.814;0.699", "P"
)
target <- tibble::tibble(
Polyphen2_HDIV_score_unparsed =
c("0.941;0.941;0.146", "1.0;1.0;0.999", "0.325;0.325;0.243",
"0.999;0.999;0.994", "0.96;0.96;0.931"),
Polyphen2_HDIV_pred_unparsed =
c("P;P;B", "D", "B", "D", "D;D;P"),
Polyphen2_HVAR_score_unparsed =
c("0.688;0.688;0.138", "0.993;0.993;0.989", "0.21;0.21;0.136",
"0.939;0.939;0.863", "0.814;0.814;0.699"),
Polyphen2_HVAR_pred_unparsed =
c("P;P;B", "D", "B", "D;D;P", "P"),
Polyphen2_HDIV_score =
c("0.941", "1", "0.325", "0.999", "0.96"),
Polyphen2_HDIV_pred =
c("P", "D", "B", "D", "D"),
Polyphen2_HVAR_score =
c("0.688", "0.993", "0.21", "0.939", "0.814"),
Polyphen2_HVAR_pred =
c("P", "D", "B", "D", "P")
)
result <- .parse_pairs_max(example,
list(c("Polyphen2_HDIV_score",
"Polyphen2_HDIV_pred"),
c("Polyphen2_HVAR_score",
"Polyphen2_HVAR_pred")))
expect_identical(result, target)
})
UW-GAC/wgsaparsr documentation built on Aug. 9, 2020, 5:50 a.m.
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context("test_.parse_pairs_max() - unit tests")
test_that(".parse_pairs_max() gives error if pair_columns is not a list", {
example <- tibble::tibble(
Eigen_PC_raw = c(".{1}", "-0.164398825586883{1}",
".{5}-0.00506108216253831{4}0.0200792355286427{1}",
".{5}0.636779480039485{1}0.651616016738356{2}", ".{5}",
".{3}0.382030178748437{1}0.394216023865136{1}",
".{3}-0.0842385276257326{1}-0.0880785370562746{1}",
".;-0.0842385276257326;-0.0880785370562746{1}"
),
fathmm_MKL_coding_score = c(".{1}", "0.87811{1}", ".{5}0.90605{5}",
".{5}0.90734{3}", ".{5}", ".{3}0.90912{2}",
".{3}0.90863{2}", "0.90863{3};0.90863{2}"),
MAP20_149bp = c("0.0{1}", "0.004166664{1}", "0.015773803{10}",
"0.01666666{8}",
"0.09196428{1}0.09553571{1}0.09732143{1}0.09910714{1}",
"0.11339285{1}0.12053571{1}0.12410714{1}0.12767857{1}",
"0.19464286{1}0.19821429{1}0.20178571{1}0.20535715{1}",
"0.19464286{1};0.19821429{1}0.20178571{1};0.20535715{1}")
)
expect_error(.parse_pairs_max(example, "not a list"),
"pair_columns must be a list")
})
test_that(".parse_pairs_max() gives error when parsing a tripple", {
example <- tibble::tibble(
Eigen_PC_raw = c(".{1}", "-0.164398825586883{1}",
".{5}-0.00506108216253831{4}0.0200792355286427{1}",
".{5}0.636779480039485{1}0.651616016738356{2}", ".{5}",
".{3}0.382030178748437{1}0.394216023865136{1}",
".{3}-0.0842385276257326{1}-0.0880785370562746{1}",
".;-0.0842385276257326;-0.0880785370562746{1}"
),
"fathmm_MKL_coding_score" = c(".{1}", "0.87811{1}", ".{5}0.90605{5}",
".{5}0.90734{3}", ".{5}", ".{3}0.90912{2}",
".{3}0.90863{2}", "0.90863{3};0.90863{2}"),
MAP20_149bp = c("0.0{1}", "0.004166664{1}", "0.015773803{10}",
"0.01666666{8}",
"0.09196428{1}0.09553571{1}0.09732143{1}0.09910714{1}",
"0.11339285{1}0.12053571{1}0.12410714{1}0.12767857{1}",
"0.19464286{1}0.19821429{1}0.20178571{1}0.20535715{1}",
"0.19464286{1};0.19821429{1}0.20178571{1};0.20535715{1}")
)
expect_error(.parse_pairs_max(example, list(c("Eigen_PC_raw",
"MAP20_149bp",
"fathmm_MKL_coding_score"))),
"pair columns not length 1 or 2")
})
test_that(".parse_pairs_max() returns expected tibble when parsing a single", {
example <- tibble::tibble(
Eigen_PC_raw = c(".{1}", "-0.164398825586883{1}",
".{5}-0.00506108216253831{4}0.0200792355286427{1}",
".{5}0.636779480039485{1}0.651616016738356{2}", ".{5}",
".{3}0.382030178748437{1}0.394216023865136{1}",
".{3}-0.0842385276257326{1}-0.0880785370562746{1}",
".;-0.0842385276257326;-0.0880785370562746{1}"
),
fathmm_MKL_coding_score = c(".{1}", "0.87811{1}", ".{5}0.90605{5}",
".{5}0.90734{3}", ".{5}", ".{3}0.90912{2}",
".{3}0.90863{2}", "0.90863{3};0.90863{2}"),
MAP20_149bp = c("0.0{1}", "0.004166664{1}", "0.015773803{10}",
"0.01666666{8}",
"0.09196428{1}0.09553571{1}0.09732143{1}0.09910714{1}",
"0.11339285{1}0.12053571{1}0.12410714{1}0.12767857{1}",
"0.19464286{1}0.19821429{1}0.20178571{1}0.20535715{1}",
"0.19464286{1};0.19821429{1}0.20178571{1};0.20535715{1}")
)
target <- tibble::tibble(
Eigen_PC_raw = c(".{1}", "-0.164398825586883{1}",
".{5}-0.00506108216253831{4}0.0200792355286427{1}",
".{5}0.636779480039485{1}0.651616016738356{2}", ".{5}",
".{3}0.382030178748437{1}0.394216023865136{1}",
".{3}-0.0842385276257326{1}-0.0880785370562746{1}",
".;-0.0842385276257326;-0.0880785370562746{1}"
),
fathmm_MKL_coding_score = c(".{1}", "0.87811{1}", ".{5}0.90605{5}",
".{5}0.90734{3}", ".{5}", ".{3}0.90912{2}",
".{3}0.90863{2}", "0.90863{3};0.90863{2}"),
# note: first value of parsed MAP20_149bp is "0", not "0.0". I think that's
# okay
MAP20_149bp = c("0", "0.004166664", "0.015773803", "0.01666666",
"0.09910714", "0.12767857", "0.20535715", "0.20535715"),
MAP20_149bp_unparsed = c("0.0{1}", "0.004166664{1}", "0.015773803{10}",
"0.01666666{8}",
"0.09196428{1}0.09553571{1}0.09732143{1}0.09910714{1}",
"0.11339285{1}0.12053571{1}0.12410714{1}0.12767857{1}",
"0.19464286{1}0.19821429{1}0.20178571{1}0.20535715{1}",
"0.19464286{1};0.19821429{1}0.20178571{1};0.20535715{1}")
)
result <- .parse_pairs_max(example, list(c("MAP20_149bp")))
expect_identical(result, target)
})
test_that(".parse_pairs_max() returns expected tibble when parsing a pair", {
example <- dplyr::tribble(
~Polyphen2_HDIV_score, ~Polyphen2_HDIV_pred, ~Polyphen2_HVAR_score,
~Polyphen2_HVAR_pred,
"0.941;0.941;0.146", "P;P;B", "0.688;0.688;0.138", "P;P;B",
"1.0;1.0;0.999", "D", "0.993;0.993;0.989", "D",
"0.325;0.325;0.243", "B", "0.21;0.21;0.136", "B",
"0.999;0.999;0.994", "D", "0.939;0.939;0.863", "D;D;P",
"0.96;0.96;0.931", "D;D;P", "0.814;0.814;0.699", "P"
)
target <- tibble::tibble(
Polyphen2_HDIV_score_unparsed =
c("0.941;0.941;0.146", "1.0;1.0;0.999", "0.325;0.325;0.243",
"0.999;0.999;0.994", "0.96;0.96;0.931"),
Polyphen2_HDIV_pred_unparsed =
c("P;P;B", "D", "B", "D", "D;D;P"),
Polyphen2_HVAR_score =
c("0.688;0.688;0.138", "0.993;0.993;0.989", "0.21;0.21;0.136",
"0.939;0.939;0.863", "0.814;0.814;0.699"),
Polyphen2_HVAR_pred =
c("P;P;B", "D", "B", "D;D;P", "P"),
Polyphen2_HDIV_score =
c("0.941", "1", "0.325", "0.999", "0.96"),
Polyphen2_HDIV_pred =
c("P", "D", "B", "D", "D")
)
result <- .parse_pairs_max(example,
list(c("Polyphen2_HDIV_score",
"Polyphen2_HDIV_pred")))
expect_identical(result, target)
})
test_that(".parse_pairs_max() returns expected tibble when parsing two pairs", {
example <- dplyr::tribble(
~Polyphen2_HDIV_score, ~Polyphen2_HDIV_pred, ~Polyphen2_HVAR_score,
~Polyphen2_HVAR_pred,
"0.941;0.941;0.146", "P;P;B", "0.688;0.688;0.138", "P;P;B",
"1.0;1.0;0.999", "D", "0.993;0.993;0.989", "D",
"0.325;0.325;0.243", "B", "0.21;0.21;0.136", "B",
"0.999;0.999;0.994", "D", "0.939;0.939;0.863", "D;D;P",
"0.96;0.96;0.931", "D;D;P", "0.814;0.814;0.699", "P"
)
target <- tibble::tibble(
Polyphen2_HDIV_score_unparsed =
c("0.941;0.941;0.146", "1.0;1.0;0.999", "0.325;0.325;0.243",
"0.999;0.999;0.994", "0.96;0.96;0.931"),
Polyphen2_HDIV_pred_unparsed =
c("P;P;B", "D", "B", "D", "D;D;P"),
Polyphen2_HVAR_score_unparsed =
c("0.688;0.688;0.138", "0.993;0.993;0.989", "0.21;0.21;0.136",
"0.939;0.939;0.863", "0.814;0.814;0.699"),
Polyphen2_HVAR_pred_unparsed =
c("P;P;B", "D", "B", "D;D;P", "P"),
Polyphen2_HDIV_score =
c("0.941", "1", "0.325", "0.999", "0.96"),
Polyphen2_HDIV_pred =
c("P", "D", "B", "D", "D"),
Polyphen2_HVAR_score =
c("0.688", "0.993", "0.21", "0.939", "0.814"),
Polyphen2_HVAR_pred =
c("P", "D", "B", "D", "P")
)
result <- .parse_pairs_max(example,
list(c("Polyphen2_HDIV_score",
"Polyphen2_HDIV_pred"),
c("Polyphen2_HVAR_score",
"Polyphen2_HVAR_pred")))
expect_identical(result, target)
})
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