tests/testthat/test-5-processBismarkAln.r
In al2na/methylKit: DNA methylation analysis from high-throughput bisulfite sequencing results
context("processBismarkAln checks")
test_that("expect that there is an error when reading an unsorted sam file", {
expect_that(
processBismarkAln(
location = system.file("extdata", "test.fastq_bismark.unsorted.min.sam",
package = "methylKit"),
sample.id = "test1",
assembly = "hg18",
verbose = FALSE
) ,
throws_error()
)
expect_that(
processBismarkAln(
location = system.file(
"extdata",
"test.fastq_bismark.unsorted_chr.min.sam",
package = "methylKit"
),
sample.id = "test1",
assembly = "hg18",
verbose = FALSE
) ,
throws_error()
)
})
test_that("check that bismark single-end bam can be read",
{
expect_is(
suppressWarnings(
processBismarkAln(
location = system.file("extdata", "test.bismark_single_end.sorted.bam", package = "methylKit"),
sample.id = "test1",
assembly = "hg18",
treatment = NULL,
verbose = FALSE
)),
'methylRaw'
)
})
test_that("check that bismark paired-end bam can be read",
{
expect_is(suppressWarnings(
processBismarkAln(
location = system.file("extdata", "ctrl.bismark_paired_end.sorted.bam", package = "methylKit"),
sample.id = "ctrl1",
assembly = "hg18",
treatment = NULL,
verbose = FALSE
)),
'methylRaw')
})
test_that("check that sam file can be read-in", {
expect_is(suppressMessages(
processBismarkAln(
location = system.file("extdata", "test.fastq_bismark.sorted.min.sam", package = "methylKit"),
sample.id = "test1",
assembly = "hg18",
verbose = FALSE
)
),
'methylRaw')
expect_is(
suppressMessages(
processBismarkAln(
location = system.file("extdata", "test.fastq_bismark.sorted.min.sam", package = "methylKit"),
sample.id = "test1",
assembly = "hg18",
save.folder = "methylDB",
save.db = TRUE,
verbose = FALSE
)),
'methylRawDB')
})
test_that("check that reading sam and bam returns the same object", {
expect_equal(
processBismarkAln(
location = system.file("extdata",
"ctrl.bismark_paired_end.sorted.bam",
package = "methylKit"
),
sample.id = "ctrl1",
assembly = "hg18",
verbose = FALSE,
mincov = 1
),
processBismarkAln(
location = system.file("extdata",
"ctrl.bismark_paired_end.sorted.wh.sam",
package = "methylKit"
),
sample.id = "ctrl1",
assembly = "hg18",
verbose = FALSE,
mincov = 1
)
)
expect_equal(
processBismarkAln(
location = system.file("extdata",
"test.bismark_single_end.sorted.bam",
package = "methylKit"
),
sample.id = "test",
assembly = "hg18",
verbose = FALSE,
mincov = 1
),
processBismarkAln(
location = system.file("extdata",
"test.bismark_single_end.sorted.wh.sam",
package = "methylKit"
),
sample.id = "test",
assembly = "hg18",
verbose = FALSE,
mincov = 1
)
)
})
test_that("check that CHG context can be read in", {
expect_is(
processBismarkAln(
location = system.file("extdata", "test.fastq_bismark.sorted.min.sam", package = "methylKit"),
sample.id = "test1",
assembly = "hg18",
read.context = "CHG",
verbose = FALSE
),
'methylRaw')
})
test_that("check that CHG context can be read-in as methylrawdb", {
expect_is(
processBismarkAln(
location = system.file("extdata", "test.fastq_bismark.sorted.min.sam", package = "methylKit"),
sample.id = "test1",
assembly = "hg18",
read.context = "CHG",
save.folder = "methylDB",
save.db = TRUE,
verbose = FALSE
),
'methylRawDB')
})
test_that("check that CHH context can be read-inas methylraw", {
expect_is(suppressMessages(
processBismarkAln(
location = system.file("extdata", "test.fastq_bismark.sorted.min.sam", package = "methylKit"),
sample.id = "test1",
assembly = "hg18",
read.context = "CHH",
verbose = FALSE
)
),
'methylRaw')
})
test_that("check that CHH context can be read-in as methylrawdb", {
expect_is(suppressWarnings(
processBismarkAln(
location = system.file("extdata", "test.fastq_bismark.sorted.min.sam", package = "methylKit"),
sample.id = "test1",
assembly = "hg18",
read.context = "CHH",
save.folder = "methylDB",
save.db = TRUE,
verbose = FALSE
)
),
'methylRawDB')
})
# reading multiple files
file.list2=list(system.file("extdata", "test.fastq_bismark.sorted.min.sam",
package = "methylKit"),
system.file("extdata", "test.fastq_bismark.sorted.min.sam",
package = "methylKit"),
system.file("extdata", "test.fastq_bismark.sorted.min.sam",
package = "methylKit"),
system.file("extdata", "test.fastq_bismark.sorted.min.sam",
package = "methylKit"))
test_that("check that multiple files can be read-in as methylrawList", {
expect_is(
processBismarkAln(
location = file.list2,
sample.id = list("test1", "test2", "ctrl1", "ctrl1"),
assembly = "hg18",
save.folder = NULL,
save.context = NULL,
read.context = "CpG",
nolap = FALSE,
mincov = 10,
minqual = 20,
phred64 = FALSE,
treatment = c(1, 1, 0, 0),
verbose = FALSE
),
'methylRawList'
)
})
# test for consistent output (see https://github.com/al2na/methylKit/issues/334)
aln_sam <-
'@HD VN:1.0 SO:coordinate
@SQ SN:chr19 LN:7000000
@PG ID:Bismark VN:v0.24.2 CL:"bismark --non_directional --parallel 8 --genome Big_Data/Test_WGBS/mapping_BOWTIE2/bismark_genome --bowtie2 --score_min L,0,-0.6 -N 0 --bam --gzip --output_dir Big_Data/Test_WGBS/mapping_BOWTIE2/bam_byName/ None -1 Big_Data/Test_WGBS/trimmed/SRR11806589_sub500000_chr19_R1_clean.fastq.gz -2 Big_Data/Test_WGBS/trimmed/SRR11806589_sub500000_chr19_R2_clean.fastq.gz"
@PG ID:samtools PN:samtools PP:Bismark VN:1.20 CL:/opt/conda/envs/methylator_v1.1_noversion/bin/samtools view -bSh -
@PG ID:samtools.1 PN:samtools PP:samtools VN:1.20 CL:/opt/conda/envs/methylator_v1.1_noversion/bin/samtools view -h /shared/projects/bi4edc/WGBSflow/Big_Data/Test_WGBS/mapping_BOWTIE2/bam_byName/SRR11806589_sub500000_chr19_R1_clean.fastq.gz.temp.1.gz_bismark_bt2_pe.bam
@PG ID:samtools.2 PN:samtools PP:samtools.1 VN:1.20 CL:/opt/conda/envs/methylator_v1.1_noversion/bin/samtools view -bSh -
@PG ID:samtools.3 PN:samtools PP:samtools.2 VN:1.20 CL:/opt/conda/envs/methylator_v1.1_noversion/bin/samtools view -h --threads 1 Big_Data/Test_WGBS/mapping_BOWTIE2/bam_byName/SRR11806589_sub500000_chr19_clean_bismark_bt2_pe.bam
@PG ID:samtools.4 PN:samtools PP:samtools.3 VN:1.20 CL:/opt/conda/envs/methylator_v1.1_noversion/bin/samtools view -bS --threads 1 -
@PG ID:samtools.5 PN:samtools PP:samtools.4 VN:1.20 CL:samtools sort -o Big_Data/Test_WGBS/mapping_BOWTIE2/Deduplicate/SRR11806589_sub500000_chr19.deduplicated.sort.bam -T tmp_SRR11806589_sub500000_chr19/ --threads 8 Big_Data/Test_WGBS/mapping_BOWTIE2/Deduplicate/SRR11806589_sub500000_chr19.deduplicated.bam
@PG ID:samtools.6 PN:samtools PP:samtools.5 VN:1.14 CL:samtools view -bh test/SRR11806589_sub500000_chr19.deduplicated.sort.bam chr19:3079455-3079616
@PG ID:samtools.7 PN:samtools PP:samtools.6 VN:1.14 CL:samtools view -h reduced.bam
SRR11806589.332334077_332334077_length=100 147 chr19 3079387 7 67M6I6M = 3079292 -168 TTTAGGAGAGGTATTGTTGGATTTTTTGGTAGTATTATGTTTAGTTTTTTGAGGAATTGTTAGATTGATTTTTATCTTC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFF:FF NM:i:25 MD:Z:0C0C0C13C5C0C1C0C7C5C0C6C7C0C1C0C3C4T1C1 XM:Z:hhx.............x.....hh.xz.......h.....hx......x.......xz.hx...x............hX XR:Z:GA XG:Z:CT
SRR11806589.332350504_332350504_length=100 163 chr19 3079399 6 81M = 3079429 111 ATTACTAAATCCTCCAATAATACTATATCCAATTTTCTAAAAAACCACCAAACTAATTTCCAAAATAATTATACAAACCTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF NM:i:21 MD:Z:3G2G0G7G0G2G6G4G6G1G0G4G3G3G7G1G1G0G2G5G3G0 XM:Z:...h..xh.......zx..h......h....x......x.hh....z...x...x.......x.h.hh..h.....h...x XR:Z:GA XG:Z:GA
SRR11806589.332355738_332355738_length=100 147 chr19 3079400 7 81M = 3079269 -212 TTGTTGGATTTTTTGGTAGTATTATGTTTAGTTTTTTGAGGAATTGTTAGATTGATTTTTAGAGTGGTTGTATAAGTCTCC FFFFFFFFF:F:FFFF:FF:FFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFF NM:i:19 MD:Z:3C5C0C1C0C7C5C0C6C7C0C1C0C3C6C0C12C3C2G1 XM:Z:...x.....hh.xz.......h.....hx......x.......xz.hx...x......hx............h...hX..H XR:Z:GA XG:Z:CT
SRR11806589.332362696_332362696_length=100 163 chr19 3079416 6 81M = 3079510 175 TAATACTATATCCAATTTTCTAAAAAACCACCAAACTAATTTCCAAAATAATTATACAAACCTACACTCCCACCAACAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFF:FF:F:FFFF,F NM:i:17 MD:Z:2G6G4G6G1G0G4G3G3G7G1G1G0G2G5G3G16G0 XM:Z:..h......h....x......x.hh....z...x...x.......x.h.hh..h.....h...x................h XR:Z:GA XG:Z:GA
SRR11806589.332370546_332370546_length=100 147 chr19 3079418 6 80M = 3079337 -161 GTATTATGTTTAGTTTTTTGAGGAATTGTTAGATTGATTTTTAGAGTGGTTGTATAAGTTTGTATTTTTATTAATAATGG FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF NM:i:22 MD:Z:3C5C0C6C7C0C1C0C3C6C0C12C3C0C2C1C1C0C0C1C0C2C5 XM:Z:...h.....hx......x.......xz.hx...x......hx............h...hx..h.h.hhh.hh..h..... XR:Z:GA XG:Z:CT
SRR11806589.216596805_216596805_length=100 163 chr19 3079419 31 65M = 3079506 153 TACTATATCCAATTTTCTAAAAAACCGCCAAACTAATTTCCAAAATAATTATACAAACCTACACT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF NM:i:14 MD:Z:6G4G6G1G0G8G3G7G1G1G0G2G5G3G4 XM:Z:......h....x......x.hh....Z...x...x.......x.h.hh..h.....h...x.... XR:Z:GA XG:Z:GA
SRR11806589.332350504_332350504_length=100 83 chr19 3079429 6 81M = 3079399 -111 AATTTTCTAAAAAACCACCAAACTAATTTCCAAAATAATTATACAAACCTACACTCCCACCAACAATAAAAAAATATTCCT FFFFFFFFFFFFFFFFFFFF:,FFF,FFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FF:FF:FFFF NM:i:20 MD:Z:1G6G1G0G4G3G3G7G1G1G0G2G5G3G16G0G1G0G1G1G5 XM:Z:.x......x.hh....z...x...x.......x.h.hh..h.....h...x................hh.hh.h.h..... XR:Z:CT XG:Z:GA
SRR11806589.332373229_332373229_length=100 163 chr19 3079442 6 81M = 3079555 192 ACCACCAAACTAATTTCCAAAATAATTATACAAACCTACACTCCCACCAACAATAAAAAAATATTCCTCTTTCTCCACATC FFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFF NM:i:16 MD:Z:3G3G3G7G1G1G0G2G5G3G16G0G1G0G1G1G18 XM:Z:...z...x...x.......x.h.hh..h.....h...x................hh.hh.h.h.................. XR:Z:GA XG:Z:GA
SRR11806589.332360085_332360085_length=100 99 chr19 3079448 12 67M = 3079569 201 AGATTGATTTTTAGAGTGGTTGTATAAGTTTGTATTTTTATTAGTAATGGAGGAGTGTTTTTTTTTT FFFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF NM:i:19 MD:Z:3C6C0C12C3C0C2C1C1C0C0C1C0C1A0C14C0C1C3C0 XM:Z:...x......hx............h...hx..h.h.hhh.hh..h..............hh.h...h XR:Z:CT XG:Z:CT
SRR11806589.332355734_332355734_length=100 99 chr19 3079450 7 55M1D26M = 3079577 207 ATTGATTTTTAGAGTGGTTGTATAAGTTTGTATTTTTATTAATAATGGAGGAGTGTTTTTTTTTTTTATATTTTCGTTAGT FF:FFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF,:F:F,F NM:i:27 MD:Z:1C6C0C12C3C0C2C1C1C0C0C1C0C2C12^T1C0C1C3C1C0C1C2C0C3A0C2C0 XM:Z:.x......hx............h...hx..h.h.hhh.hh..h.............hh.h...h.hh.h..hh.Z..x..h XR:Z:CT XG:Z:CT
SRR11806589.332369609_332369609_length=100 163 chr19 3079467 7 41M2D40M = 3079525 137 TTATACAAACCTACAATCCCACCAACAATAAAAAAATATTCCTTTCTCCACATCCTCAACAACATCTACTATCACCTAAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF NM:i:17 MD:Z:2G5G3G2C13G0G1G0G1G1G3^CT16G3G5G2G6G3 XM:Z:..h.....h...x................hh.hh.h.h...................z...x.....x..x......x... XR:Z:GA XG:Z:GA
SRR11806589.332334753_332334753_length=100 99 chr19 3079483 6 22M1I58M = 3079639 237 TTTTATTAATAATGGAGGAGTGTTTTTTTTTTTTTTATATTTTTGTTAGTATTTGTTGTTATTTGAATTTTTGATTTTAGT FFFFFFFFFFFF:FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,FFFFFFFFFFFFFFFFF,, NM:i:27 MD:Z:1C0C0C1C0C2C14C0C1C3C1C0C1C2C0C1C1A0C2C2C2C3C1C0C12C4C0 XM:Z:.hhh.hh..h...............hh.h...h.hh.h..hh.z..x..h..x..x...h.hx............h....h XR:Z:CT XG:Z:CT
SRR11806589.332331913_332331913_length=100 99 chr19 3079502 6 80M = 3079563 142 GTGTTTTTTTTTTTTTATATTTTTGATAGTATTTGTTGTTATTTGAATTTTTGATTTTAGTTATTTTGATTGGTGTGAGG FFFFFFFFFFFFFFFFFFF,FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFF:FFFFF:FFFFF NM:i:22 MD:Z:5C0C1C3C1C0C1C2C0C1C2C2C2C2C3C1C0C12C4C0C3C3C10 XM:Z:.....hh.h...h.hh.h..hh.z..x..h..x..x...h.hx............h....hh...x...x.......... XR:Z:CT XG:Z:CT
SRR11806589.216596805_216596805_length=100 83 chr19 3079506 31 66M = 3079419 -153 TCCTCTTTCTCCACATCCTCGACAACATCTACTATCACCTAAATTTTTAATCTTAACCATTCTAAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:::F,FFFFF:F NM:i:7 MD:Z:24G5G2G6G7G6G7G2 XM:Z:....................Z...x.....x..x......x.......h......h.......x.. XR:Z:CT XG:Z:GA
SRR11806589.332362696_332362696_length=100 83 chr19 3079510 6 81M = 3079416 -175 CTTTCTCCACATCCTCACCAACATCTACTATCACCTAAATTTTTAATCTTAACCATTCTAACTAATATAAAATAAAATCTC FFFFFFFFFFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF NM:i:17 MD:Z:16G0A2G5G2G6G7G6G7G3G0G1G1G1G0G1G0G6 XM:Z:................z...x.....x..x......x.......h......h.......x...xh.h.h.hh.hh...... XR:Z:CT XG:Z:GA
SRR11806589.332369609_332369609_length=100 83 chr19 3079525 7 79M = 3079467 -137 CAACAACATCTACTATCACCTAAATTTTTAATCTTAACCATTCTAACTAATATAAAATAAAATCTCAAAATTATTTTAA FF:FFFFFFFFFFF:FFFFFFFFFFFF,FFFF::FFFFFFFFF:F:FFFF:FFFFFFFFF:FFFFFFFFFFFFFFFFFF NM:i:21 MD:Z:1G3G5G2G6G7G6G7G3G0G1G1G1G0G1G0G7G0G0G2G4G1 XM:Z:.z...x.....x..x......x.......h......h.......x...xh.h.h.hh.hh.......xhh..h....h. XR:Z:CT XG:Z:GA
SRR11806589.332335201_332335201_length=100 163 chr19 3079536 6 80M = 3079610 154 ACTATCACCTAAATTTTTAATCTTAACCATTCTAACTAATATAAAATAAAATCTCAAAATTATTTTAATTTACATTTCCC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFF NM:i:20 MD:Z:0G2G6G7G6G7G3G0G1G1G1G0G1G0G7G0G0G2G4G4G8 XM:Z:x..x......x.......h......h.......x...xh.h.h.hh.hh.......xhh..h....h....h........ XR:Z:GA XG:Z:GA
SRR11806589.332359309_332359309_length=100 163 chr19 3079551 2 81M = 3079605 134 GAGAATCTTAACCATTCTAACTAATATAAAATAAAATCTCAAAATTATTTTAATTTACATTTCCCTATTAATTAAAAATAT FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF NM:i:26 MD:Z:0T0T0T0G6G7G3G0G1G1G1G0G1G0G7G0G0G2G4G4G9G0A1G5G0G2G1 XM:Z:...h......h.......x...xh.h.h.hh.hh.......xhh..h....h....h.........x..h.....hh..h. XR:Z:GA XG:Z:GA
SRR11806589.332373229_332373229_length=100 83 chr19 3079555 6 79M = 3079442 -192 ATCTTAACCATTCTAACTAATATAAAATAAAATCTCAAAATTATTTTAATTTACATTTCCCTAATAATTAAAAATATTA FFFFFFFFFFF:FFF,FFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF NM:i:22 MD:Z:6G7G3G0G1G1G1G0G1G0G7G0G0G2G4G4G9G2G5G0G2G2G0 XM:Z:......h.......x...xh.h.h.hh.hh.......xhh..h....h....h.........x..h.....hh..h..h XR:Z:CT XG:Z:GA
SRR11806589.332374487_332374487_length=100 163 chr19 3079559 2 38M1D42M = 3079653 174 TCCCCATTCTAACTAATATAAAATAAAATCTCAATATTTTTTAATTTACATTTCCCTAATAATTAAAAATACTAAACATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF:F NM:i:24 MD:Z:1A0G7G3G0G1G1G1G0G1G0G7G0G0G2^G4G4G9G2G5G0G2G0T1G6 XM:Z:..........x...xh.h.h.hh.hh.......x.h......h....h.........x..h.....hh..h..h...... XR:Z:GA XG:Z:GA
SRR11806589.332331913_332331913_length=100 147 chr19 3079563 6 81M = 3079502 -142 TATTTTGATTGGTGTGAGGTGGAATTTTAGGGTTGTTTTGATTTGTATTTTATTGATGATTAAGGATGTTGAATATTTTTT FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF NM:i:10 MD:Z:0C3C3C16C1C17C4C0C0C20C7 XM:Z:h...x...x................h.x.................h....h.x....................h....... XR:Z:GA XG:Z:CT
SRR11806589.332360085_332360085_length=100 147 chr19 3079569 12 80M = 3079448 -201 GATTGGTGTGAGGTGGAATTTTAGGGTTGTTTTGATTTGTATTTTTTTGATGATTAAGGATGTTGAATATTTTTTTAAGT FFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF NM:i:9 MD:Z:2C16C1C17C4C0C0C20C7C4 XM:Z:..x................h.x.................h....hhx....................h.......h.... XR:Z:GA XG:Z:CT
SRR11806589.332355734_332355734_length=100 147 chr19 3079577 7 80M = 3079450 -207 TGAGGTGGAATATTAGGGTTGTTTTGATTTGTATTTTTTTGATGATTAAGGATGTTGAATATTTTTTTAAGTGTTTTTTT FFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF NM:i:11 MD:Z:11C1C17C4C0C0C20C7C5C2C1C1 XM:Z:.............x.................h....hhx....................h.......h.....h..h.x. XR:Z:GA XG:Z:CT
SRR11806589.332348899_332348899_length=100 99 chr19 3079600 6 80M = 3079656 135 TTGATTTGTATTTTTTTGATGATTAAGGATTTTGAGTATTTTTTTAAGTGTTTTTTTGTTATTTGGTATTTTTTAGGTGA FF,FFFFFFFF,:FFFFFFF,FFFFF:FFF,FF,FFFFFFF,F:FFFF:FFFFFFFF:FFF::FFFFFFFF:FFFF,:FF NM:i:17 MD:Z:8C4C0C0C14G4A0C7C5C2C1C2C0C3C6C0C1C6 XM:Z:........h....hhx....................h.......h.....h..h.x..hh...z......hh.x...... XR:Z:CT XG:Z:CT
SRR11806589.332359309_332359309_length=100 83 chr19 3079605 2 80M = 3079551 -134 TTACATTTCCCTATTAATTAAAAATATTAAACATTTTTTCAAATACTTCTCTACCATTCGATATTACTCAAATAAAAATT FFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF NM:i:17 MD:Z:2G9G0A1G5G0G2G2G13G1G7G7G4C4G0G1G1G4 XM:Z:..h.........x..h.....hh..h..h.............h.h.......x......Zx.........xh.h.h.... XR:Z:CT XG:Z:GA
SRR11806589.332356300_332356300_length=100 163 chr19 3079610 2 80M = 3079795 261 TTTCCCTAATGATTAAAAATACTAAACATTTTTTCAAATACTTCTCTACCATTCGATATTCCTCAAATAAAAATTCTTCG :F:FF:FFF:FFF,FFF,F:FFFF:FFF,FF,FFFFFFFF,FF:F:F:,FF:FFFFFF,FFF:FFFF:FFFFF,::F:FF NM:i:15 MD:Z:7G8G0G2G0T1G13G1G7G7G9G0G1G1G7T1 XM:Z:.......x..H.....hh..h..h.............h.h.......x......Zx.........xh.h.h........H XR:Z:GA XG:Z:GA
SRR11806589.332335201_332335201_length=100 83 chr19 3079610 6 80M = 3079536 -154 TTTCCCTAATAATTAAAAATATTAAACATTTTTTCAAATACTTCTCTACCATTCAATATTCCTCAAATAAAAATTCTTTA FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFF NM:i:16 MD:Z:7G2G5G0G2G2G13G1G7G6G0G9G0G1G1G8G0 XM:Z:.......x..h.....hh..h..h.............h.h.......x......zx.........xh.h.h........h XR:Z:CT XG:Z:GA'
writeLines(aln_sam,con = "aln.sam")
aln_out <-
'"chr","start","end","strand","coverage","numCs","numTs"
"chr19",3079413,3079413,"+",2,0,2
"chr19",3079414,3079414,"-",1,0,1
"chr19",3079444,3079444,"+",3,0,3
"chr19",3079445,3079445,"-",4,1,3
"chr19",3079525,3079525,"+",2,0,2
"chr19",3079526,3079526,"-",4,1,3
"chr19",3079663,3079663,"+",1,0,1
"chr19",3079664,3079664,"-",3,2,1'
aln_df <- read.csv(text = aln_out,header = TRUE, sep = ",")
test_that("check that output is consisten with methylKit.1.20.0", {
expect_identical(
getData(
processBismarkAln(
location ="aln.sam",
sample.id = "test",
assembly = "mm39",
save.folder = NULL,
save.context = NULL,
read.context = "CpG",
nolap = FALSE,
mincov = 1,
minqual = 20,
phred64 = FALSE,
treatment = 0,
verbose = FALSE
)
),
aln_df
)
})
unlink("aln.sam")
unlink("tests/testthat/methylDB",recursive = TRUE)
al2na/methylKit documentation built on Jan. 12, 2025, 7:56 a.m.
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context("processBismarkAln checks")
test_that("expect that there is an error when reading an unsorted sam file", {
expect_that(
processBismarkAln(
location = system.file("extdata", "test.fastq_bismark.unsorted.min.sam",
package = "methylKit"),
sample.id = "test1",
assembly = "hg18",
verbose = FALSE
) ,
throws_error()
)
expect_that(
processBismarkAln(
location = system.file(
"extdata",
"test.fastq_bismark.unsorted_chr.min.sam",
package = "methylKit"
),
sample.id = "test1",
assembly = "hg18",
verbose = FALSE
) ,
throws_error()
)
})
test_that("check that bismark single-end bam can be read",
{
expect_is(
suppressWarnings(
processBismarkAln(
location = system.file("extdata", "test.bismark_single_end.sorted.bam", package = "methylKit"),
sample.id = "test1",
assembly = "hg18",
treatment = NULL,
verbose = FALSE
)),
'methylRaw'
)
})
test_that("check that bismark paired-end bam can be read",
{
expect_is(suppressWarnings(
processBismarkAln(
location = system.file("extdata", "ctrl.bismark_paired_end.sorted.bam", package = "methylKit"),
sample.id = "ctrl1",
assembly = "hg18",
treatment = NULL,
verbose = FALSE
)),
'methylRaw')
})
test_that("check that sam file can be read-in", {
expect_is(suppressMessages(
processBismarkAln(
location = system.file("extdata", "test.fastq_bismark.sorted.min.sam", package = "methylKit"),
sample.id = "test1",
assembly = "hg18",
verbose = FALSE
)
),
'methylRaw')
expect_is(
suppressMessages(
processBismarkAln(
location = system.file("extdata", "test.fastq_bismark.sorted.min.sam", package = "methylKit"),
sample.id = "test1",
assembly = "hg18",
save.folder = "methylDB",
save.db = TRUE,
verbose = FALSE
)),
'methylRawDB')
})
test_that("check that reading sam and bam returns the same object", {
expect_equal(
processBismarkAln(
location = system.file("extdata",
"ctrl.bismark_paired_end.sorted.bam",
package = "methylKit"
),
sample.id = "ctrl1",
assembly = "hg18",
verbose = FALSE,
mincov = 1
),
processBismarkAln(
location = system.file("extdata",
"ctrl.bismark_paired_end.sorted.wh.sam",
package = "methylKit"
),
sample.id = "ctrl1",
assembly = "hg18",
verbose = FALSE,
mincov = 1
)
)
expect_equal(
processBismarkAln(
location = system.file("extdata",
"test.bismark_single_end.sorted.bam",
package = "methylKit"
),
sample.id = "test",
assembly = "hg18",
verbose = FALSE,
mincov = 1
),
processBismarkAln(
location = system.file("extdata",
"test.bismark_single_end.sorted.wh.sam",
package = "methylKit"
),
sample.id = "test",
assembly = "hg18",
verbose = FALSE,
mincov = 1
)
)
})
test_that("check that CHG context can be read in", {
expect_is(
processBismarkAln(
location = system.file("extdata", "test.fastq_bismark.sorted.min.sam", package = "methylKit"),
sample.id = "test1",
assembly = "hg18",
read.context = "CHG",
verbose = FALSE
),
'methylRaw')
})
test_that("check that CHG context can be read-in as methylrawdb", {
expect_is(
processBismarkAln(
location = system.file("extdata", "test.fastq_bismark.sorted.min.sam", package = "methylKit"),
sample.id = "test1",
assembly = "hg18",
read.context = "CHG",
save.folder = "methylDB",
save.db = TRUE,
verbose = FALSE
),
'methylRawDB')
})
test_that("check that CHH context can be read-inas methylraw", {
expect_is(suppressMessages(
processBismarkAln(
location = system.file("extdata", "test.fastq_bismark.sorted.min.sam", package = "methylKit"),
sample.id = "test1",
assembly = "hg18",
read.context = "CHH",
verbose = FALSE
)
),
'methylRaw')
})
test_that("check that CHH context can be read-in as methylrawdb", {
expect_is(suppressWarnings(
processBismarkAln(
location = system.file("extdata", "test.fastq_bismark.sorted.min.sam", package = "methylKit"),
sample.id = "test1",
assembly = "hg18",
read.context = "CHH",
save.folder = "methylDB",
save.db = TRUE,
verbose = FALSE
)
),
'methylRawDB')
})
# reading multiple files
file.list2=list(system.file("extdata", "test.fastq_bismark.sorted.min.sam",
package = "methylKit"),
system.file("extdata", "test.fastq_bismark.sorted.min.sam",
package = "methylKit"),
system.file("extdata", "test.fastq_bismark.sorted.min.sam",
package = "methylKit"),
system.file("extdata", "test.fastq_bismark.sorted.min.sam",
package = "methylKit"))
test_that("check that multiple files can be read-in as methylrawList", {
expect_is(
processBismarkAln(
location = file.list2,
sample.id = list("test1", "test2", "ctrl1", "ctrl1"),
assembly = "hg18",
save.folder = NULL,
save.context = NULL,
read.context = "CpG",
nolap = FALSE,
mincov = 10,
minqual = 20,
phred64 = FALSE,
treatment = c(1, 1, 0, 0),
verbose = FALSE
),
'methylRawList'
)
})
# test for consistent output (see https://github.com/al2na/methylKit/issues/334)
aln_sam <-
'@HD VN:1.0 SO:coordinate
@SQ SN:chr19 LN:7000000
@PG ID:Bismark VN:v0.24.2 CL:"bismark --non_directional --parallel 8 --genome Big_Data/Test_WGBS/mapping_BOWTIE2/bismark_genome --bowtie2 --score_min L,0,-0.6 -N 0 --bam --gzip --output_dir Big_Data/Test_WGBS/mapping_BOWTIE2/bam_byName/ None -1 Big_Data/Test_WGBS/trimmed/SRR11806589_sub500000_chr19_R1_clean.fastq.gz -2 Big_Data/Test_WGBS/trimmed/SRR11806589_sub500000_chr19_R2_clean.fastq.gz"
@PG ID:samtools PN:samtools PP:Bismark VN:1.20 CL:/opt/conda/envs/methylator_v1.1_noversion/bin/samtools view -bSh -
@PG ID:samtools.1 PN:samtools PP:samtools VN:1.20 CL:/opt/conda/envs/methylator_v1.1_noversion/bin/samtools view -h /shared/projects/bi4edc/WGBSflow/Big_Data/Test_WGBS/mapping_BOWTIE2/bam_byName/SRR11806589_sub500000_chr19_R1_clean.fastq.gz.temp.1.gz_bismark_bt2_pe.bam
@PG ID:samtools.2 PN:samtools PP:samtools.1 VN:1.20 CL:/opt/conda/envs/methylator_v1.1_noversion/bin/samtools view -bSh -
@PG ID:samtools.3 PN:samtools PP:samtools.2 VN:1.20 CL:/opt/conda/envs/methylator_v1.1_noversion/bin/samtools view -h --threads 1 Big_Data/Test_WGBS/mapping_BOWTIE2/bam_byName/SRR11806589_sub500000_chr19_clean_bismark_bt2_pe.bam
@PG ID:samtools.4 PN:samtools PP:samtools.3 VN:1.20 CL:/opt/conda/envs/methylator_v1.1_noversion/bin/samtools view -bS --threads 1 -
@PG ID:samtools.5 PN:samtools PP:samtools.4 VN:1.20 CL:samtools sort -o Big_Data/Test_WGBS/mapping_BOWTIE2/Deduplicate/SRR11806589_sub500000_chr19.deduplicated.sort.bam -T tmp_SRR11806589_sub500000_chr19/ --threads 8 Big_Data/Test_WGBS/mapping_BOWTIE2/Deduplicate/SRR11806589_sub500000_chr19.deduplicated.bam
@PG ID:samtools.6 PN:samtools PP:samtools.5 VN:1.14 CL:samtools view -bh test/SRR11806589_sub500000_chr19.deduplicated.sort.bam chr19:3079455-3079616
@PG ID:samtools.7 PN:samtools PP:samtools.6 VN:1.14 CL:samtools view -h reduced.bam
SRR11806589.332334077_332334077_length=100 147 chr19 3079387 7 67M6I6M = 3079292 -168 TTTAGGAGAGGTATTGTTGGATTTTTTGGTAGTATTATGTTTAGTTTTTTGAGGAATTGTTAGATTGATTTTTATCTTC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFF:FF NM:i:25 MD:Z:0C0C0C13C5C0C1C0C7C5C0C6C7C0C1C0C3C4T1C1 XM:Z:hhx.............x.....hh.xz.......h.....hx......x.......xz.hx...x............hX XR:Z:GA XG:Z:CT
SRR11806589.332350504_332350504_length=100 163 chr19 3079399 6 81M = 3079429 111 ATTACTAAATCCTCCAATAATACTATATCCAATTTTCTAAAAAACCACCAAACTAATTTCCAAAATAATTATACAAACCTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF NM:i:21 MD:Z:3G2G0G7G0G2G6G4G6G1G0G4G3G3G7G1G1G0G2G5G3G0 XM:Z:...h..xh.......zx..h......h....x......x.hh....z...x...x.......x.h.hh..h.....h...x XR:Z:GA XG:Z:GA
SRR11806589.332355738_332355738_length=100 147 chr19 3079400 7 81M = 3079269 -212 TTGTTGGATTTTTTGGTAGTATTATGTTTAGTTTTTTGAGGAATTGTTAGATTGATTTTTAGAGTGGTTGTATAAGTCTCC FFFFFFFFF:F:FFFF:FF:FFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFF NM:i:19 MD:Z:3C5C0C1C0C7C5C0C6C7C0C1C0C3C6C0C12C3C2G1 XM:Z:...x.....hh.xz.......h.....hx......x.......xz.hx...x......hx............h...hX..H XR:Z:GA XG:Z:CT
SRR11806589.332362696_332362696_length=100 163 chr19 3079416 6 81M = 3079510 175 TAATACTATATCCAATTTTCTAAAAAACCACCAAACTAATTTCCAAAATAATTATACAAACCTACACTCCCACCAACAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFF:FF:F:FFFF,F NM:i:17 MD:Z:2G6G4G6G1G0G4G3G3G7G1G1G0G2G5G3G16G0 XM:Z:..h......h....x......x.hh....z...x...x.......x.h.hh..h.....h...x................h XR:Z:GA XG:Z:GA
SRR11806589.332370546_332370546_length=100 147 chr19 3079418 6 80M = 3079337 -161 GTATTATGTTTAGTTTTTTGAGGAATTGTTAGATTGATTTTTAGAGTGGTTGTATAAGTTTGTATTTTTATTAATAATGG FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF NM:i:22 MD:Z:3C5C0C6C7C0C1C0C3C6C0C12C3C0C2C1C1C0C0C1C0C2C5 XM:Z:...h.....hx......x.......xz.hx...x......hx............h...hx..h.h.hhh.hh..h..... XR:Z:GA XG:Z:CT
SRR11806589.216596805_216596805_length=100 163 chr19 3079419 31 65M = 3079506 153 TACTATATCCAATTTTCTAAAAAACCGCCAAACTAATTTCCAAAATAATTATACAAACCTACACT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF NM:i:14 MD:Z:6G4G6G1G0G8G3G7G1G1G0G2G5G3G4 XM:Z:......h....x......x.hh....Z...x...x.......x.h.hh..h.....h...x.... XR:Z:GA XG:Z:GA
SRR11806589.332350504_332350504_length=100 83 chr19 3079429 6 81M = 3079399 -111 AATTTTCTAAAAAACCACCAAACTAATTTCCAAAATAATTATACAAACCTACACTCCCACCAACAATAAAAAAATATTCCT FFFFFFFFFFFFFFFFFFFF:,FFF,FFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FF:FF:FFFF NM:i:20 MD:Z:1G6G1G0G4G3G3G7G1G1G0G2G5G3G16G0G1G0G1G1G5 XM:Z:.x......x.hh....z...x...x.......x.h.hh..h.....h...x................hh.hh.h.h..... XR:Z:CT XG:Z:GA
SRR11806589.332373229_332373229_length=100 163 chr19 3079442 6 81M = 3079555 192 ACCACCAAACTAATTTCCAAAATAATTATACAAACCTACACTCCCACCAACAATAAAAAAATATTCCTCTTTCTCCACATC FFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFF NM:i:16 MD:Z:3G3G3G7G1G1G0G2G5G3G16G0G1G0G1G1G18 XM:Z:...z...x...x.......x.h.hh..h.....h...x................hh.hh.h.h.................. XR:Z:GA XG:Z:GA
SRR11806589.332360085_332360085_length=100 99 chr19 3079448 12 67M = 3079569 201 AGATTGATTTTTAGAGTGGTTGTATAAGTTTGTATTTTTATTAGTAATGGAGGAGTGTTTTTTTTTT FFFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF NM:i:19 MD:Z:3C6C0C12C3C0C2C1C1C0C0C1C0C1A0C14C0C1C3C0 XM:Z:...x......hx............h...hx..h.h.hhh.hh..h..............hh.h...h XR:Z:CT XG:Z:CT
SRR11806589.332355734_332355734_length=100 99 chr19 3079450 7 55M1D26M = 3079577 207 ATTGATTTTTAGAGTGGTTGTATAAGTTTGTATTTTTATTAATAATGGAGGAGTGTTTTTTTTTTTTATATTTTCGTTAGT FF:FFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF,:F:F,F NM:i:27 MD:Z:1C6C0C12C3C0C2C1C1C0C0C1C0C2C12^T1C0C1C3C1C0C1C2C0C3A0C2C0 XM:Z:.x......hx............h...hx..h.h.hhh.hh..h.............hh.h...h.hh.h..hh.Z..x..h XR:Z:CT XG:Z:CT
SRR11806589.332369609_332369609_length=100 163 chr19 3079467 7 41M2D40M = 3079525 137 TTATACAAACCTACAATCCCACCAACAATAAAAAAATATTCCTTTCTCCACATCCTCAACAACATCTACTATCACCTAAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF NM:i:17 MD:Z:2G5G3G2C13G0G1G0G1G1G3^CT16G3G5G2G6G3 XM:Z:..h.....h...x................hh.hh.h.h...................z...x.....x..x......x... XR:Z:GA XG:Z:GA
SRR11806589.332334753_332334753_length=100 99 chr19 3079483 6 22M1I58M = 3079639 237 TTTTATTAATAATGGAGGAGTGTTTTTTTTTTTTTTATATTTTTGTTAGTATTTGTTGTTATTTGAATTTTTGATTTTAGT FFFFFFFFFFFF:FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,FFFFFFFFFFFFFFFFF,, NM:i:27 MD:Z:1C0C0C1C0C2C14C0C1C3C1C0C1C2C0C1C1A0C2C2C2C3C1C0C12C4C0 XM:Z:.hhh.hh..h...............hh.h...h.hh.h..hh.z..x..h..x..x...h.hx............h....h XR:Z:CT XG:Z:CT
SRR11806589.332331913_332331913_length=100 99 chr19 3079502 6 80M = 3079563 142 GTGTTTTTTTTTTTTTATATTTTTGATAGTATTTGTTGTTATTTGAATTTTTGATTTTAGTTATTTTGATTGGTGTGAGG FFFFFFFFFFFFFFFFFFF,FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFF:FFFFF:FFFFF NM:i:22 MD:Z:5C0C1C3C1C0C1C2C0C1C2C2C2C2C3C1C0C12C4C0C3C3C10 XM:Z:.....hh.h...h.hh.h..hh.z..x..h..x..x...h.hx............h....hh...x...x.......... XR:Z:CT XG:Z:CT
SRR11806589.216596805_216596805_length=100 83 chr19 3079506 31 66M = 3079419 -153 TCCTCTTTCTCCACATCCTCGACAACATCTACTATCACCTAAATTTTTAATCTTAACCATTCTAAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:::F,FFFFF:F NM:i:7 MD:Z:24G5G2G6G7G6G7G2 XM:Z:....................Z...x.....x..x......x.......h......h.......x.. XR:Z:CT XG:Z:GA
SRR11806589.332362696_332362696_length=100 83 chr19 3079510 6 81M = 3079416 -175 CTTTCTCCACATCCTCACCAACATCTACTATCACCTAAATTTTTAATCTTAACCATTCTAACTAATATAAAATAAAATCTC FFFFFFFFFFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF NM:i:17 MD:Z:16G0A2G5G2G6G7G6G7G3G0G1G1G1G0G1G0G6 XM:Z:................z...x.....x..x......x.......h......h.......x...xh.h.h.hh.hh...... XR:Z:CT XG:Z:GA
SRR11806589.332369609_332369609_length=100 83 chr19 3079525 7 79M = 3079467 -137 CAACAACATCTACTATCACCTAAATTTTTAATCTTAACCATTCTAACTAATATAAAATAAAATCTCAAAATTATTTTAA FF:FFFFFFFFFFF:FFFFFFFFFFFF,FFFF::FFFFFFFFF:F:FFFF:FFFFFFFFF:FFFFFFFFFFFFFFFFFF NM:i:21 MD:Z:1G3G5G2G6G7G6G7G3G0G1G1G1G0G1G0G7G0G0G2G4G1 XM:Z:.z...x.....x..x......x.......h......h.......x...xh.h.h.hh.hh.......xhh..h....h. XR:Z:CT XG:Z:GA
SRR11806589.332335201_332335201_length=100 163 chr19 3079536 6 80M = 3079610 154 ACTATCACCTAAATTTTTAATCTTAACCATTCTAACTAATATAAAATAAAATCTCAAAATTATTTTAATTTACATTTCCC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFF NM:i:20 MD:Z:0G2G6G7G6G7G3G0G1G1G1G0G1G0G7G0G0G2G4G4G8 XM:Z:x..x......x.......h......h.......x...xh.h.h.hh.hh.......xhh..h....h....h........ XR:Z:GA XG:Z:GA
SRR11806589.332359309_332359309_length=100 163 chr19 3079551 2 81M = 3079605 134 GAGAATCTTAACCATTCTAACTAATATAAAATAAAATCTCAAAATTATTTTAATTTACATTTCCCTATTAATTAAAAATAT FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF NM:i:26 MD:Z:0T0T0T0G6G7G3G0G1G1G1G0G1G0G7G0G0G2G4G4G9G0A1G5G0G2G1 XM:Z:...h......h.......x...xh.h.h.hh.hh.......xhh..h....h....h.........x..h.....hh..h. XR:Z:GA XG:Z:GA
SRR11806589.332373229_332373229_length=100 83 chr19 3079555 6 79M = 3079442 -192 ATCTTAACCATTCTAACTAATATAAAATAAAATCTCAAAATTATTTTAATTTACATTTCCCTAATAATTAAAAATATTA FFFFFFFFFFF:FFF,FFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF NM:i:22 MD:Z:6G7G3G0G1G1G1G0G1G0G7G0G0G2G4G4G9G2G5G0G2G2G0 XM:Z:......h.......x...xh.h.h.hh.hh.......xhh..h....h....h.........x..h.....hh..h..h XR:Z:CT XG:Z:GA
SRR11806589.332374487_332374487_length=100 163 chr19 3079559 2 38M1D42M = 3079653 174 TCCCCATTCTAACTAATATAAAATAAAATCTCAATATTTTTTAATTTACATTTCCCTAATAATTAAAAATACTAAACATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF:F NM:i:24 MD:Z:1A0G7G3G0G1G1G1G0G1G0G7G0G0G2^G4G4G9G2G5G0G2G0T1G6 XM:Z:..........x...xh.h.h.hh.hh.......x.h......h....h.........x..h.....hh..h..h...... XR:Z:GA XG:Z:GA
SRR11806589.332331913_332331913_length=100 147 chr19 3079563 6 81M = 3079502 -142 TATTTTGATTGGTGTGAGGTGGAATTTTAGGGTTGTTTTGATTTGTATTTTATTGATGATTAAGGATGTTGAATATTTTTT FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF NM:i:10 MD:Z:0C3C3C16C1C17C4C0C0C20C7 XM:Z:h...x...x................h.x.................h....h.x....................h....... XR:Z:GA XG:Z:CT
SRR11806589.332360085_332360085_length=100 147 chr19 3079569 12 80M = 3079448 -201 GATTGGTGTGAGGTGGAATTTTAGGGTTGTTTTGATTTGTATTTTTTTGATGATTAAGGATGTTGAATATTTTTTTAAGT FFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF NM:i:9 MD:Z:2C16C1C17C4C0C0C20C7C4 XM:Z:..x................h.x.................h....hhx....................h.......h.... XR:Z:GA XG:Z:CT
SRR11806589.332355734_332355734_length=100 147 chr19 3079577 7 80M = 3079450 -207 TGAGGTGGAATATTAGGGTTGTTTTGATTTGTATTTTTTTGATGATTAAGGATGTTGAATATTTTTTTAAGTGTTTTTTT FFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF NM:i:11 MD:Z:11C1C17C4C0C0C20C7C5C2C1C1 XM:Z:.............x.................h....hhx....................h.......h.....h..h.x. XR:Z:GA XG:Z:CT
SRR11806589.332348899_332348899_length=100 99 chr19 3079600 6 80M = 3079656 135 TTGATTTGTATTTTTTTGATGATTAAGGATTTTGAGTATTTTTTTAAGTGTTTTTTTGTTATTTGGTATTTTTTAGGTGA FF,FFFFFFFF,:FFFFFFF,FFFFF:FFF,FF,FFFFFFF,F:FFFF:FFFFFFFF:FFF::FFFFFFFF:FFFF,:FF NM:i:17 MD:Z:8C4C0C0C14G4A0C7C5C2C1C2C0C3C6C0C1C6 XM:Z:........h....hhx....................h.......h.....h..h.x..hh...z......hh.x...... XR:Z:CT XG:Z:CT
SRR11806589.332359309_332359309_length=100 83 chr19 3079605 2 80M = 3079551 -134 TTACATTTCCCTATTAATTAAAAATATTAAACATTTTTTCAAATACTTCTCTACCATTCGATATTACTCAAATAAAAATT FFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF NM:i:17 MD:Z:2G9G0A1G5G0G2G2G13G1G7G7G4C4G0G1G1G4 XM:Z:..h.........x..h.....hh..h..h.............h.h.......x......Zx.........xh.h.h.... XR:Z:CT XG:Z:GA
SRR11806589.332356300_332356300_length=100 163 chr19 3079610 2 80M = 3079795 261 TTTCCCTAATGATTAAAAATACTAAACATTTTTTCAAATACTTCTCTACCATTCGATATTCCTCAAATAAAAATTCTTCG :F:FF:FFF:FFF,FFF,F:FFFF:FFF,FF,FFFFFFFF,FF:F:F:,FF:FFFFFF,FFF:FFFF:FFFFF,::F:FF NM:i:15 MD:Z:7G8G0G2G0T1G13G1G7G7G9G0G1G1G7T1 XM:Z:.......x..H.....hh..h..h.............h.h.......x......Zx.........xh.h.h........H XR:Z:GA XG:Z:GA
SRR11806589.332335201_332335201_length=100 83 chr19 3079610 6 80M = 3079536 -154 TTTCCCTAATAATTAAAAATATTAAACATTTTTTCAAATACTTCTCTACCATTCAATATTCCTCAAATAAAAATTCTTTA FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFF NM:i:16 MD:Z:7G2G5G0G2G2G13G1G7G6G0G9G0G1G1G8G0 XM:Z:.......x..h.....hh..h..h.............h.h.......x......zx.........xh.h.h........h XR:Z:CT XG:Z:GA'
writeLines(aln_sam,con = "aln.sam")
aln_out <-
'"chr","start","end","strand","coverage","numCs","numTs"
"chr19",3079413,3079413,"+",2,0,2
"chr19",3079414,3079414,"-",1,0,1
"chr19",3079444,3079444,"+",3,0,3
"chr19",3079445,3079445,"-",4,1,3
"chr19",3079525,3079525,"+",2,0,2
"chr19",3079526,3079526,"-",4,1,3
"chr19",3079663,3079663,"+",1,0,1
"chr19",3079664,3079664,"-",3,2,1'
aln_df <- read.csv(text = aln_out,header = TRUE, sep = ",")
test_that("check that output is consisten with methylKit.1.20.0", {
expect_identical(
getData(
processBismarkAln(
location ="aln.sam",
sample.id = "test",
assembly = "mm39",
save.folder = NULL,
save.context = NULL,
read.context = "CpG",
nolap = FALSE,
mincov = 1,
minqual = 20,
phred64 = FALSE,
treatment = 0,
verbose = FALSE
)
),
aln_df
)
})
unlink("aln.sam")
unlink("tests/testthat/methylDB",recursive = TRUE)
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