tests/testthat/test_align_fastq.R

In debdagybra/IMIabgd: Analyze Tcells data with mixcr and vdjtools

# context("check the align_fastq_to_vdjca function")

# align_fastq_to_vdjca ----
# test_that("align_fastq_to_vdjca gives correct command to console with R1_R2", {
#   expect_equal(
#     align_fastq_to_vdjca(
#       java_param = "java -Xmx4g -Xms3g -jar",
#       path_mixcr = "D:/Maria/Maria_Analysis/mixcr-2.1.7/mixcr.jar",
#       input_dir = "D:/Projets R/IMIabgd/data/Gamma_SR11-20/70-SR13-Gamma_S70-6542654654221/",
#       input_filename = "70-SR13-Gamma_S70_L001_R1_001.fastq.gz",
#       report_name = "alignmentReport",
#       replace = FALSE,
#       string_only = TRUE
#     ),
#     paste0(
#       "java -Xmx4g -Xms3g -jar  D:/Maria/Maria_Analysis/mixcr-2.1.7/mixcr.jar ",
#       "align -OvParameters.geneFeatureToAlign=VTranscript --report alignmentReport.log  ",
#       "70-SR13-Gamma_S70_L001_R1_001.fastq.gz 70-SR13-Gamma_S70_L001_R2_001.fastq.gz ",
#       "70-SR13-Gamma_S70_L001_R1R2_001.vdjca"
#     )
#   )
# })

# test_that("align_fastq_to_vdjca gives correct command to console with R1 only", {
#   skip("align_fastq_to_vdjca gives correct command to console with R1 only")
#   # to do with files in data_raw
#   # expect_equal(
#   #   align_fastq_to_vdjca(
#   #     java_param = "java -Xmx4g -Xms3g -jar",
#   #     path_mixcr = "D:/Maria/Maria_Analysis/mixcr-2.1.7/mixcr.jar",
#   #     input_dir = "D:/Projets R/IMIabgd/data/Gamma_SR11-20/70-SR13-Gamma_S70-6542654654221/",
#   #     input_filename = "70-SR13-Gamma_S70_L001_R1_001.fastq.gz",
#   #     report_name = "alignmentReport",
#   #     replace = FALSE,
#   #     string_only = TRUE
#   #   ),
#   #   paste0(
#   #     "java -Xmx4g -Xms3g -jar  D:/Maria/Maria_Analysis/mixcr-2.1.7/mixcr.jar ",
#   #     "align -OvParameters.geneFeatureToAlign=VTranscript --report alignmentReport.log  ",
#   #     "70-SR13-Gamma_S70_L001_R1_001.fastq.gz 70-SR13-Gamma_S70_L001_R2_001.fastq.gz ",
#   #     "70-SR13-Gamma_S70_L001_R1R2_001.vdjca"
#   #   )
#   # )
# })

# test_that("align_fastq_to_vdjca gives an error if `input_filename` is only an R2 file", {
#   skip("align_fastq_to_vdjca gives an error if `input_filename` is only an R2 file")
#   # to do with files in data_raw
#   # expect_error(
#   #   align_fastq_to_vdjca(
#   #     java_param = "java -Xmx4g -Xms3g -jar",
#   #     path_mixcr = "D:/Maria/Maria_Analysis/mixcr-2.1.7/mixcr.jar",
#   #     input_dir = "D:/Projets R/IMIabgd/data/Gamma_SR11-20/70-SR13-Gamma_S70-6542654654221/",
#   #     input_filename = "doenst_exist.fastq.gz",
#   #     report_name = "alignmentReport",
#   #     replace = FALSE,
#   #     string_only = TRUE
#   #   ),
#   #   "`input_filename` must be a valid file in `input_dir` directory."
#   # )
# })
#
# test_that("align_fastq_to_vdjca gives an error if `input_filename` doesn't exist in `input_dir`", {
#   expect_error(
#     align_fastq_to_vdjca(
#       java_param = "java -Xmx4g -Xms3g -jar",
#       path_mixcr = "D:/Maria/Maria_Analysis/mixcr-2.1.7/mixcr.jar",
#       input_dir = "D:/Projets R/IMIabgd/data/Gamma_SR11-20/70-SR13-Gamma_S70-6542654654221/",
#       input_filename = "doenst_exist.fastq.gz",
#       report_name = "alignmentReport",
#       replace = FALSE,
#       string_only = TRUE
#     ),
#     "`input_filename` must be a valid file in `input_dir` directory."
#   )
# })