mm39 excluderanges download

gist_mm39_excluderanges.R

# Download a list of problematic regions (aka blacklist) for the GRCm39/mm39 
# mouse genome assembly. Defined by the Boyle-Lab/Blacklist 
# software, High Signal and Low Mappability regions. 
# See https://github.com/dozmorovlab/excluderanges for more information.

suppressMessages(library(httr)) # https://CRAN.R-project.org/package=httr
suppressMessages(library(GenomicRanges)) # https://bioconductor.org/packages/GenomicRanges/
# bedbase_id
bedbase_id <- "edc716833d4b5ee75c34a0692fc353d5"
# Construct output file name
fileNameOut <- "mm39.excluderanges.bed.gz"
# API token for BED data
token2 <- paste0("http://bedbase.org/api/bed/", bedbase_id, "/file/bed")
# Download file
GET(url = token2, write_disk(fileNameOut, overwrite = TRUE))
# Read the data in
mm39.excluderanges <- readr::read_tsv(fileNameOut, 
                                     col_names = FALSE,
                                     col_types = c("cddcdc"))
# Assign column names depending on the number of columns
all_columns <- c("chr", "start", "end", "name", "score", "strand",
                 "signalValue", "pValue", "qValue", "peak")
colnames(mm39.excluderanges) <- all_columns[1:ncol(mm39.excluderanges)]
# Convert to GRanges object
mm39.excluderanges <- makeGRangesFromDataFrame(mm39.excluderanges, 
                                              keep.extra.columns = TRUE)
# Seqinfo for mm39 genome
chrom_data <- GenomeInfoDb::getChromInfoFromUCSC(genome = "mm39", 
                                                 assembled.molecules.only = TRUE)
# Subset and match to chromosomes in the mm39.excluderanges object
# Common chromosomes
chromosomes_common <- intersect(chrom_data$chrom, seqlevels(mm39.excluderanges))
# Subset mm39.excluderanges
mm39.excluderanges <- keepSeqlevels(mm39.excluderanges, chromosomes_common, 
                                    pruning.mode = "tidy")      
# Subset chrom_data
chrom_data <- chrom_data[chrom_data$chrom %in% chromosomes_common, ]
# Match objects
chrom_data <- chrom_data[match(seqlevels(mm39.excluderanges), chrom_data$chrom), ]
# Assign seqinfo data
seqlengths(mm39.excluderanges) <- chrom_data$size
isCircular(mm39.excluderanges) <- ifelse(is.na(chrom_data$circular), FALSE, TRUE)
genome(mm39.excluderanges)     <- "mm39"

mm39.excluderanges

Opes my bad. Here is the edited code.

`suppressMessages(library(httr)) # https://CRAN.R-project.org/package=httr
suppressMessages(library(GenomicRanges)) # https://bioconductor.org/packages/GenomicRanges/
library(readr)

bedbase_id

bedbase_id <- "edc716833d4b5ee75c34a0692fc353d5"

Construct output file name

fileNameOut <- "mm39.excluderanges.bed"

API token for BED data

#token2 <- paste0("http://bedbase.org/api/bed/", bedbase_id, "/file/bed")

Download file

#GET(url = token2, write_disk(fileNameOut, overwrite = TRUE))

Read the data in

mm39.excluderanges <- readr::read_tsv(fileNameOut,
col_names = FALSE)

Assign column names depending on the number of columns

all_columns <- c("chr", "start", "end", "name", "strand","score",
"signalValue", "pValue", "qValue", "peak")
colnames(mm39.excluderanges) <- all_columns[1:ncol(mm39.excluderanges)]

Convert to GRanges object

mm39.excluderanges <- makeGRangesFromDataFrame(mm39.excluderanges,
keep.extra.columns = TRUE)

Seqinfo for mm39 genome

chrom_data <- GenomeInfoDb::getChromInfoFromUCSC(genome = "mm39",
assembled.molecules.only = TRUE)

Subset and match to chromosomes in the mm39.excluderanges object

Common chromosomes

chromosomes_common <- intersect(chrom_data$chrom, seqlevels(mm39.excluderanges))

Subset mm39.excluderanges

mm39.excluderanges <- keepSeqlevels(mm39.excluderanges, chromosomes_common,
pruning.mode = "tidy")

Subset chrom_data

chrom_data <- chrom_data[chrom_data$chrom %in% chromosomes_common, ]

Match objects

chrom_data <- chrom_data[match(seqlevels(mm39.excluderanges), chrom_data$chrom), ]

Assign seqinfo data

seqlengths(mm39.excluderanges) <- chrom_data$size
isCircular(mm39.excluderanges) <- ifelse(is.na(chrom_data$circular), FALSE, TRUE)
genome(mm39.excluderanges) <- "mm39"

mm39.excluderanges

bed<- as.data.frame(mm39.excluderanges)

Rename columns

colnames(bed) <- c("chrom", "chromStart", "chromEnd", "width", "strand", "score", "name")

Reorder columns

bed_2 <- bed[, c("chrom", "chromStart", "chromEnd", "name", "score", "strand")]

write.table( bed, file = "mm39.excluderanges_2.bed",
sep = "\t", row.names = FALSE, col.names = FALSE, quote = FALSE)`