Skip to content

Commit

Permalink
test without static files
Browse files Browse the repository at this point in the history
  • Loading branch information
@philippadoherty
philippadoherty committed Sep 19, 2024
1 parent 483032f commit d877f45
Show file tree
Hide file tree
Showing 3 changed files with 101 additions and 102 deletions.
2 changes: 1 addition & 1 deletion DESCRIPTION
View file
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Package: MACSr
Title: MACS: Model-based Analysis for ChIP-Seq
Version: 1.11.3
Version: 1.13.1
Authors@R: c(
person(given = "Philippa",
family = "Doherty",
Expand Down
5 changes: 2 additions & 3 deletions NEWS
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,3 @@
Changes in version 1.11.3 (2024-9-12)
Changes in version 1.13.1 (2024-9-19)
+ Upgrade to MACS 3.0.2.
Changes in version 1.11.2 (2023-11-20)
+ Upgrade to MACS 3.0.0.

196 changes: 98 additions & 98 deletions tests/testthat/test-init.R
View file
Original file line number Diff line number Diff line change
@@ -1,13 +1,13 @@

# datdir <- system.file("extdata", package = "MACSr")
# eh <- ExperimentHub::ExperimentHub()
# eh <- AnnotationHub::query(eh, "MACSdata")
# CHIP <- eh[["EH4558"]]
# CTRL <- eh[["EH4563"]]
# CHIPPE <- eh[["EH4559"]]
# CTRLPE <- eh[["EH4564"]]
# CHIPBEDPE <- eh[["EH4560"]]
# CTRLBEDPE <- eh[["EH4565"]]
datdir <- system.file("extdata", package = "MACSr")
eh <- ExperimentHub::ExperimentHub()
eh <- AnnotationHub::query(eh, "MACSdata")
CHIP <- eh[["EH4558"]]
CTRL <- eh[["EH4563"]]
CHIPPE <- eh[["EH4559"]]
CTRLPE <- eh[["EH4564"]]
CHIPBEDPE <- eh[["EH4560"]]
CTRLBEDPE <- eh[["EH4565"]]


# context("1. test callpeak")
Expand Down Expand Up @@ -113,16 +113,16 @@


## atac <- hmmratac(bam=ATACSEQBAM, outdir="/tmp/atac", name="hmmratac_yeast500k", save_train=TRUE)
datdir <- system.file("extdata", package = "MACSr")
# datdir <- system.file("extdata", package = "MACSr")

CHIP <- file.path(datdir, "CTCF_SE_ChIP_chr22_50k.bed.gz")
CTRL <- file.path(datdir, "CTCF_SE_CTRL_chr22_50k.bed.gz")
# CHIP <- file.path(datdir, "CTCF_SE_ChIP_chr22_50k.bed.gz")
# CTRL <- file.path(datdir, "CTCF_SE_CTRL_chr22_50k.bed.gz")

CHIPPE <- file.path(datdir, "CTCF_PE_ChIP_chr22_50k.bam")
CTRLPE <- file.path(datdir, "CTCF_PE_CTRL_chr22_50k.bam")
# CHIPPE <- file.path(datdir, "CTCF_PE_ChIP_chr22_50k.bam")
# CTRLPE <- file.path(datdir, "CTCF_PE_CTRL_chr22_50k.bam")

CHIPBEDPE <- file.path(datdir, "CTCF_PE_ChIP_chr22_50k.bedpe.gz")
CTRLBEDPE <- file.path(datdir, "CTCF_PE_CTRL_chr22_50k.bedpe.gz")
# CHIPBEDPE <- file.path(datdir, "CTCF_PE_ChIP_chr22_50k.bedpe.gz")
# CTRLBEDPE <- file.path(datdir, "CTCF_PE_CTRL_chr22_50k.bedpe.gz")


context("1. test callpeak")
Expand Down Expand Up @@ -173,19 +173,19 @@ context("5. test randsample")
outputfile = "randsample_output.bed"))
})

context("6. test refinepeak")
test_that("refinepeak runs without error 1", {
expect_no_error(rp1 <- refinepeak(
bedfile = file.path(datdir, 'run_callpeak_narrow0_peaks.narrowPeak'),
ifile = CHIP,
oprefix="refinepeak_output_prefix"))
})
test_that("refinepeak runs without error 2", {
expect_no_error(rp2 <- refinepeak(
bedfile = file.path(datdir, 'run_callpeak_narrow0_peaks.narrowPeak'),
ifile = CHIP,
outputfile="refinepeak_output.bed"))
})
# context("6. test refinepeak")
# test_that("refinepeak runs without error 1", {
# expect_no_error(rp1 <- refinepeak(
# bedfile = file.path(datdir, 'run_callpeak_narrow0_peaks.narrowPeak'),
# ifile = CHIP,
# oprefix="refinepeak_output_prefix"))
# })
# test_that("refinepeak runs without error 2", {
# expect_no_error(rp2 <- refinepeak(
# bedfile = file.path(datdir, 'run_callpeak_narrow0_peaks.narrowPeak'),
# ifile = CHIP,
# outputfile="refinepeak_output.bed"))
# })

context("7. test bdgcmp")
test_that("bdgcmp runs without error 1", {
Expand All @@ -205,63 +205,63 @@ context("7. test bdgcmp")
outputfile= list("bdgcmp_output.bdg") )) # why is it defined as a list?
})

context("8. test bdgpeakcall")
test_that("bdgpeakcall runs without error 1", {
expect_no_error(bdgpc1 <- bdgpeakcall(
ifile = file.path(datdir, 'run_bdgcmp_FE.bdg'),
cutoff = 2,
oprefix="bdgpeakcall_output_prefix"))
})
test_that("bdgpeakcall runs without error 2", {
expect_no_error(bdgpc2 <- bdgpeakcall(
ifile = file.path(datdir, 'run_bdgcmp_FE.bdg'),
cutoff = 2,
outputfile="bdgpeakcall_output.txt"))
})

context("9. test bdgbroadcall")
test_that("bdgbroadcall runs without error 1", {
expect_no_error(bdgbc1 <- bdgbroadcall(
ifile = file.path(datdir, 'run_bdgcmp_FE.bdg'),
cutoffpeak=2,
cutofflink=1.5,
oprefix="bdgbroadcall_output" ))
})
test_that("bdgbroadcall runs without error 2", {
expect_no_error(bdgbc2 <- bdgbroadcall(
ifile = file.path(datdir, 'run_bdgcmp_FE.bdg'),
cutoffpeak=2,
cutofflink=1.5,
outputfile="bdgbroadcall_output.bed" ))
})

context("10. test bdgdiff")
test_that("bdgdiff runs without error 1", {
expect_no_error(bdgdiff1 <- bdgdiff(
t1bdg = file.path(datdir, 'run_callpeak_narrow0_treat_pileup.bdg'),
c1bdg = file.path(datdir, 'run_callpeak_narrow0_control_lambda.bdg'),
t2bdg = file.path(datdir, 'run_callpeak_narrow_revert_treat_pileup.bdg'),
c2bdg = file.path(datdir, 'run_callpeak_narrow_revert_control_lambda.bdg'),
oprefix="bdgdiff_output_prefix"))
})
test_that("bdgdiff runs without error 2", {
expect_no_error(bdgdiff2 <- bdgdiff(
t1bdg = file.path(datdir, 'run_callpeak_narrow0_treat_pileup.bdg'),
c1bdg = file.path(datdir, 'run_callpeak_narrow0_control_lambda.bdg'),
t2bdg = file.path(datdir, 'run_callpeak_narrow_revert_treat_pileup.bdg'),
c2bdg = file.path(datdir, 'run_callpeak_narrow_revert_control_lambda.bdg'),
outputfile= list("bdgdiff_output1.bed", "bdgdiff_output2.bed", "bdgdiff_output3.bed")))
})

context("11. test cmbreps")
test_that("cmbreps runs without error", {
expect_no_error(cmbreps <- cmbreps(
ifile = list(file.path(datdir, 'run_callpeak_narrow0_treat_pileup.bdg'),
file.path(datdir, 'run_callpeak_narrow0_control_lambda.bdg')),
method = "max",
outputfile = "cmbreps_output.bdg"
))
})
# context("8. test bdgpeakcall")
# test_that("bdgpeakcall runs without error 1", {
# expect_no_error(bdgpc1 <- bdgpeakcall(
# ifile = file.path(datdir, 'run_bdgcmp_FE.bdg'),
# cutoff = 2,
# oprefix="bdgpeakcall_output_prefix"))
# })
# test_that("bdgpeakcall runs without error 2", {
# expect_no_error(bdgpc2 <- bdgpeakcall(
# ifile = file.path(datdir, 'run_bdgcmp_FE.bdg'),
# cutoff = 2,
# outputfile="bdgpeakcall_output.txt"))
# })

# context("9. test bdgbroadcall")
# test_that("bdgbroadcall runs without error 1", {
# expect_no_error(bdgbc1 <- bdgbroadcall(
# ifile = file.path(datdir, 'run_bdgcmp_FE.bdg'),
# cutoffpeak=2,
# cutofflink=1.5,
# oprefix="bdgbroadcall_output" ))
# })
# test_that("bdgbroadcall runs without error 2", {
# expect_no_error(bdgbc2 <- bdgbroadcall(
# ifile = file.path(datdir, 'run_bdgcmp_FE.bdg'),
# cutoffpeak=2,
# cutofflink=1.5,
# outputfile="bdgbroadcall_output.bed" ))
# })

# context("10. test bdgdiff")
# test_that("bdgdiff runs without error 1", {
# expect_no_error(bdgdiff1 <- bdgdiff(
# t1bdg = file.path(datdir, 'run_callpeak_narrow0_treat_pileup.bdg'),
# c1bdg = file.path(datdir, 'run_callpeak_narrow0_control_lambda.bdg'),
# t2bdg = file.path(datdir, 'run_callpeak_narrow_revert_treat_pileup.bdg'),
# c2bdg = file.path(datdir, 'run_callpeak_narrow_revert_control_lambda.bdg'),
# oprefix="bdgdiff_output_prefix"))
# })
# test_that("bdgdiff runs without error 2", {
# expect_no_error(bdgdiff2 <- bdgdiff(
# t1bdg = file.path(datdir, 'run_callpeak_narrow0_treat_pileup.bdg'),
# c1bdg = file.path(datdir, 'run_callpeak_narrow0_control_lambda.bdg'),
# t2bdg = file.path(datdir, 'run_callpeak_narrow_revert_treat_pileup.bdg'),
# c2bdg = file.path(datdir, 'run_callpeak_narrow_revert_control_lambda.bdg'),
# outputfile= list("bdgdiff_output1.bed", "bdgdiff_output2.bed", "bdgdiff_output3.bed")))
# })

# context("11. test cmbreps")
# test_that("cmbreps runs without error", {
# expect_no_error(cmbreps <- cmbreps(
# ifile = list(file.path(datdir, 'run_callpeak_narrow0_treat_pileup.bdg'),
# file.path(datdir, 'run_callpeak_narrow0_control_lambda.bdg')),
# method = "max",
# outputfile = "cmbreps_output.bdg"
# ))
# })

context("12. test bdgopt")
test_that("bdgopt runs without error", {
Expand All @@ -284,17 +284,17 @@ context("13. test callvar")

# context("14. test 50k contigs with buffersize")

context("15. test hmmratac")
test_that("hmmratac runs without error, defaults", {
expect_no_error(hm1 <- hmmratac(
input_file = file.path(datdir, 'yeast_500k_SRR1822137.bam'),
name = "hmmratac_output"))
})
test_that("hmmratac runs without error, format = BEDPE", {
expect_no_error(hm2 <- hmmratac(
input_file = file.path(datdir, 'yeast_500k_SRR1822137.bedpe.gz'),
format = 'BEDPE',
name = "hmmratac_bedpe_output"))
})
# context("15. test hmmratac")
# test_that("hmmratac runs without error, defaults", {
# expect_no_error(hm1 <- hmmratac(
# input_file = file.path(datdir, 'yeast_500k_SRR1822137.bam'),
# name = "hmmratac_output"))
# })
# test_that("hmmratac runs without error, format = BEDPE", {
# expect_no_error(hm2 <- hmmratac(
# input_file = file.path(datdir, 'yeast_500k_SRR1822137.bedpe.gz'),
# format = 'BEDPE',
# name = "hmmratac_bedpe_output"))
# })


0 comments on commit d877f45

Please sign in to comment.