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Added tests for parse_MaxQuant #25
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jenzopr
suggested changes
Jul 12, 2018
tests/testthat/summary_test.txt
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| @@ -0,0 +1,3 @@ | |||
| Raw file Experiment | |||
| Bernd baut bemüht bienen bei blumenbergen Exp1 | |||
| Dieter drückt daknbar den dünnen Daniel durch die dicke dauerbelstete Dachrinne Exp2 | |||
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ups.. that was the wrong test file :D
tests/testthat/summary_test_2.txt
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| Raw file False | |||
| Bernd baut bemüht bienen bei blumenbergen Exp1 | |||
| Dieter drückt daknbar den dünnen Daniel durch die dicke dauerbelastete Dachrinne Exp2 | |||
R/parser.R
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| @@ -286,6 +299,8 @@ parse_MaxQuant <- function(proteinGroups_in, summary_in, outfile, outfile_reduce | |||
| # writing reduced CLARION file | |||
| write_clarion_file(meta = meta_reduced, out = outfile_reduced, format = format, | |||
| version = version, exp_id = experiment_id, pGroups = proteinGroups, delimiter = delimiter) | |||
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| return(1) | |||
R/parser.R
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| @@ -25,6 +25,8 @@ | |||
| #' @param version pre-header information about version (optional) | |||
| #' @param experiment_id pre-header information about experiment id (optional) | |||
| #' | |||
| #' @return 1 on success | |||
jenzopr
approved these changes
Jul 12, 2018
HendrikSchultheis
suggested changes
Jul 13, 2018
tests/testthat/test_mqparser.R
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| context("MaxQuant parser") | |||
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| testthat::test_that("all needed input parameteres are given", { | |||
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The :: notation is not needed for wilson and testthat. The packages are both loaded before testing
R/parser.R
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| # getting experiment names | ||
| exp_names <- (unique(summary_file[Experiment != "", Experiment])) | ||
| if("Experiment" %in% colnames(summary_file)){ |
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Add whitespace after 'if' and before '{'. Like this:
if ("Experiment" %in% colnames(summary_file)) {
R/parser.R
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| # getting experiment names | ||
| exp_names <- (unique(summary_file[Experiment != "", Experiment])) | ||
| if("Experiment" %in% colnames(summary_file)){ | ||
| exp_names <- (unique(summary_file[Experiment != "", Experiment])) |
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The outer brackets are redundant.
R/parser.R
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| meta <- get_meta_from_config(meta_config = meta_config) | ||
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Don't follow an empty line with another empty line.
R/parser.R
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| @@ -188,13 +190,21 @@ parse_MaxQuant <- function(proteinGroups_in, summary_in, outfile, outfile_reduce | |||
| # reading files in data tables | |||
| proteinGroups <- data.table::fread(proteinGroups_in, header = TRUE, quote = "") | |||
| summary_file <- data.table::fread(summary_in, header = TRUE) | |||
| meta_config <- rjson::fromJSON(file = config) | |||
| meta_config <- tryCatch({rjson::fromJSON(file = config)}, | |||
| error=function(cond){ | |||
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Add whitespace around '=' and before '{'.
R/parser.R
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| @@ -203,6 +213,9 @@ parse_MaxQuant <- function(proteinGroups_in, summary_in, outfile, outfile_reduce | |||
| sample_ary <- meta_config$type_array | |||
| reduced_list <- meta_config$reduced_list | |||
| full_sample_list <- c(sample_scores, sample_ratios, sample_probability, sample_category, sample_ary) | |||
| if(is.null(reduced_list)){ | |||
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Add whitespaces.
HendrikSchultheis
approved these changes
Jul 16, 2018
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