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added mapping to ensembl chrom names in fetchExtendedChromInfoFromUCSC #5

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merged 3 commits into from
Dec 20, 2019
Merged

added mapping to ensembl chrom names in fetchExtendedChromInfoFromUCSC #5

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fbc5e9a
added mapping to ensembl chromosome names in fetchExtendedChromInfoFr…
ivanek Dec 21, 2018
0b7e7b8
improved method for obtaining Ensembl_seqlevel in fetchExtendedChromI…
ivanek Jan 8, 2019
5ec34b2
merged after reslving issue in R/fetchExtendedChromInfoFromUCSC.R
ivanek Feb 18, 2019
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121 changes: 100 additions & 21 deletions R/fetchExtendedChromInfoFromUCSC.R
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Original file line number Diff line number Diff line change
Expand Up @@ -7,16 +7,22 @@
### Some low-level helpers.
###

fetch_ChromInfo_from_UCSC <- function(genome,
fetch_table_from_UCSC <- function(genome, table="chromInfo", colnames,
goldenPath_url="http://hgdownload.cse.ucsc.edu/goldenPath")
{
url <- paste(goldenPath_url, genome, "database/chromInfo.txt.gz", sep="/")
url <- paste(goldenPath_url, genome, "database", paste0(table, ".txt.gz"), sep="/")
destfile <- tempfile()
download.file(url, destfile, quiet=TRUE)
colnames <- c("chrom", "size", "fileName")
read.table(destfile, sep="\t", quote="",
col.names=colnames, comment.char="",
stringsAsFactors=FALSE)
if (missing(colnames)) {
read.table(destfile, sep="\t", quote="",
comment.char="",
stringsAsFactors=FALSE)
} else {
read.table(destfile, sep="\t", quote="",
col.names=colnames,
comment.char="",
stringsAsFactors=FALSE)
}
}

### Used in BSgenome!
Expand Down Expand Up @@ -174,6 +180,46 @@ fetch_GenBankAccn2seqlevel_from_NCBI <- function(assembly, AssemblyUnits=NULL)
ans
}

fetch_ensembl_chromNames_from_UCSC <- function(genome, chromAliases, UCSC_seqlevels, duplicated_contigs)
{
ensembl_seqlevels <- rep(NA_character_, length(UCSC_seqlevels))
names(ensembl_seqlevels) <- UCSC_seqlevels

## 1. fill in what is already provided by the package `GenomeInfoDb`
org <- suppressWarnings(mapGenomeBuilds(genome)[1,"organism"])
if (!is.null(org)) {
## org2 <- .normalize_organism(org)
## available_orgs <- names(.getNamedFiles())
## if (org2 %in% available_orgs) {
chroms <- try(genomeStyles(org), silent=TRUE)
if (!is(chroms, "try-error")) {
chroms <- chroms[chroms$UCSC %in% names(ensembl_seqlevels),]
ensembl_seqlevels[chroms$UCSC] <- chroms$Ensembl
}
}

## 2. fetch info from UCSC
for (tbl in chromAliases) {
uscs_seqlevels_without_ensembl <- names(ensembl_seqlevels)[which(is.na(ensembl_seqlevels))]
if (length(uscs_seqlevels_without_ensembl)) {
if (tbl == "chromAlias") {
colnames <- c("alias", "chrom", "source")
} else if (tbl == "ucscToEnsembl") {
colnames <- c("chrom","alias")
}
chroms <- fetch_table_from_UCSC(genome, colnames=colnames, table=tbl)
if ("source" %in% colnames(chroms)) {
chroms <- chroms[grep("ensembl", chroms[,"source"]),c("chrom", "alias")]
}
chroms <- chroms[!chroms$alias %in% duplicated_contigs,]
rownames(chroms) <- chroms$chrom
uscs_seqlevels_without_ensembl <- uscs_seqlevels_without_ensembl[uscs_seqlevels_without_ensembl %in% rownames(chroms)]
ensembl_seqlevels[uscs_seqlevels_without_ensembl] <- chroms[uscs_seqlevels_without_ensembl, "alias"]
}
}
as.character(ensembl_seqlevels)
}

standard_fetch_extended_ChromInfo_from_UCSC <- function(
genome,
circ_seqs,
Expand All @@ -183,9 +229,13 @@ standard_fetch_extended_ChromInfo_from_UCSC <- function(
unmapped_seqs,
drop_unmapped,
goldenPath_url,
chromAliases,
duplicated_contigs,
quiet)
{
chrominfo <- fetch_ChromInfo_from_UCSC(genome,
chrominfo <- fetch_table_from_UCSC(genome,
table="chromInfo",
colnames=c("chrom", "size", "fileName"),
goldenPath_url=goldenPath_url)
UCSC_seqlevel <- chrominfo[ , "chrom"]
circular_idx <- match(circ_seqs, UCSC_seqlevel)
Expand All @@ -202,6 +252,7 @@ standard_fetch_extended_ChromInfo_from_UCSC <- function(
if (!quiet)
warning(wmsg(genome, " UCSC genome is not based on ",
"an NCBI assembly"))

oo <- order(rankSeqlevels(ans[ , "UCSC_seqlevel"]))
ans <- ans[oo, , drop=FALSE]
rownames(ans) <- NULL
Expand Down Expand Up @@ -279,6 +330,12 @@ standard_fetch_extended_ChromInfo_from_UCSC <- function(
unmapped_idx <- match(unmapped_seqs, ans[ , "UCSC_seqlevel"])
ans[sort(unmapped_idx), ] <- ans[unmapped_idx, , drop=FALSE]
}
## add mapping to ensembl chromosomes from UCSC tables
Ensembl_seqlevel <- fetch_ensembl_chromNames_from_UCSC(genome=genome,
chromAliases=chromAliases, UCSC_seqlevels=ans$UCSC_seqlevel,
duplicated_contigs=duplicated_contigs)
if (!all(is.na(Ensembl_seqlevel)))
ans <- cbind(ans, Ensembl_seqlevel, stringsAsFactors=FALSE)
rownames(ans) <- NULL
ans
}
Expand All @@ -293,6 +350,7 @@ SUPPORTED_UCSC_GENOMES <- list(
circ_seqs="chrM",
assembly_accession="GCF_000001405.26",
special_mappings=c(chrM="MT"),
get_Ensembl_seqlevels_from=c("chromAlias","ucscToEnsembl"),
## The chromInfo table at UCSC contains sequences that belong to
## GRCh38.p12 but not to GRCh38. Because we want to map hg38 to
## GRCh38 and not to GRCh38.p12, we drop these sequences.
Expand All @@ -313,7 +371,8 @@ SUPPORTED_UCSC_GENOMES <- list(
chr6_qbl_hap6="HSCHR6_MHC_QBL_CTG1",
chr6_ssto_hap7="HSCHR6_MHC_SSTO_CTG1",
chr17_ctg5_hap1="HSCHR17_1_CTG5"),
unmapped_seqs=list(`assembled-molecule`="chrM")
unmapped_seqs=list(`assembled-molecule`="chrM"),
get_Ensembl_seqlevels_from=c("chromAlias","ucscToEnsembl")
),

hg18=list(
Expand All @@ -327,14 +386,16 @@ SUPPORTED_UCSC_GENOMES <- list(
`pseudo-scaffold`=paste0("chr",
c("5_h2_hap1", "6_qbl_hap2",
paste0(c((1:22)[-c(12, 14, 20)], "X"), "_random"))))
## , get_Ensembl_seqlevels_from="ucscToEnsembl"
),

### Chimp
panTro4=list(
FUN="standard_fetch_extended_ChromInfo_from_UCSC",
circ_seqs="chrM",
assembly_accession="GCF_000001515.5",
special_mappings=c(chrM="MT")
special_mappings=c(chrM="MT"),
get_Ensembl_seqlevels_from=c("chromAlias","ucscToEnsembl")
),

panTro3=list(
Expand All @@ -360,7 +421,8 @@ SUPPORTED_UCSC_GENOMES <- list(
FUN="standard_fetch_extended_ChromInfo_from_UCSC",
circ_seqs="chrM",
assembly_accession="GCF_000003055.5",
special_mappings=c(chrM="MT")
special_mappings=c(chrM="MT"),
get_Ensembl_seqlevels_from="chromAlias"
),

bosTau7=list(
Expand All @@ -374,7 +436,8 @@ SUPPORTED_UCSC_GENOMES <- list(
FUN="standard_fetch_extended_ChromInfo_from_UCSC",
circ_seqs="chrM",
assembly_accession="GCF_000003055.4",
special_mappings=c(chrM="MT")
special_mappings=c(chrM="MT"),
get_Ensembl_seqlevels_from=c("chromAlias","ucscToEnsembl")
),

### Dog
Expand All @@ -385,7 +448,8 @@ SUPPORTED_UCSC_GENOMES <- list(
special_mappings=c(chr1="chr01", chr2="chr02", chr3="chr03",
chr4="chr04", chr5="chr05", chr6="chr06",
chr7="chr07", chr8="chr08", chr9="chr09",
chrM="MT")
chrM="MT"),
get_Ensembl_seqlevels_from="chromAlias"
),

canFam2=list(
Expand All @@ -401,7 +465,8 @@ SUPPORTED_UCSC_GENOMES <- list(
### Ferret
musFur1=list(
FUN="standard_fetch_extended_ChromInfo_from_UCSC",
assembly_accession="GCF_000215625.1"
assembly_accession="GCF_000215625.1",
get_Ensembl_seqlevels_from="chromAlias"
),

### Mouse
Expand All @@ -410,7 +475,8 @@ SUPPORTED_UCSC_GENOMES <- list(
circ_seqs="chrM",
assembly_accession="GCF_000001635.20",
AssemblyUnits=c("C57BL/6J", "non-nuclear"),
special_mappings=c(chrM="MT")
special_mappings=c(chrM="MT"),
get_Ensembl_seqlevels_from=c("chromAlias","ucscToEnsembl")
),

mm9=list(
Expand Down Expand Up @@ -440,7 +506,8 @@ SUPPORTED_UCSC_GENOMES <- list(
FUN="standard_fetch_extended_ChromInfo_from_UCSC",
circ_seqs="chrM",
assembly_accession="GCF_000003025.5",
special_mappings=c(chrM="MT")
special_mappings=c(chrM="MT"),
get_Ensembl_seqlevels_from="chromAlias"
),

susScr2=list(
Expand All @@ -455,7 +522,11 @@ SUPPORTED_UCSC_GENOMES <- list(
FUN="standard_fetch_extended_ChromInfo_from_UCSC",
circ_seqs="chrM",
assembly_accession="GCF_000001895.5",
special_mappings=c(chrM="MT")
special_mappings=c(chrM="MT"),
get_Ensembl_seqlevels_from="chromAlias"
## https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/rn6.txt
## LINES 856:864
, duplicated_contigs=c("AABR07023006.1","AABR07022518.1")
),

### Rhesus
Expand All @@ -479,7 +550,8 @@ SUPPORTED_UCSC_GENOMES <- list(
assembly_accession="GCF_000002315.3",
special_mappings=c(chrLGE22C19W28_E50C23="ChrE22C19W28_E50C23",
chrLGE64="ChrE64",
chrM="MT")
chrM="MT"),
get_Ensembl_seqlevels_from=c("chromAlias","ucscToEnsembl")
),

galGal3=list(
Expand All @@ -498,8 +570,9 @@ SUPPORTED_UCSC_GENOMES <- list(
### Stickleback
gasAcu1=list(
FUN="standard_fetch_extended_ChromInfo_from_UCSC",
circ_seqs="chrM"
circ_seqs="chrM",
#assembly_accession="GCA_000180675.1"
get_Ensembl_seqlevels_from="chromAlias"
),

### Zebra finch
Expand All @@ -522,7 +595,8 @@ SUPPORTED_UCSC_GENOMES <- list(
FUN="standard_fetch_extended_ChromInfo_from_UCSC",
circ_seqs="chrM",
assembly_accession="GCF_000002035.4",
special_mappings=c(chrM="MT")
special_mappings=c(chrM="MT"),
get_Ensembl_seqlevels_from="chromAlias"
),

#Too messy!
Expand All @@ -546,7 +620,9 @@ SUPPORTED_UCSC_GENOMES <- list(
FUN="standard_fetch_extended_ChromInfo_from_UCSC",
circ_seqs="chrM",
assembly_accession="GCF_000001215.4",
special_mappings=c(chrM="MT")
## special_mappings=c(chrM="MT"),
special_mappings=c(chrM="mitochondrion_genome"),
get_Ensembl_seqlevels_from="chromAlias"
),

dm3=list(
Expand Down Expand Up @@ -585,7 +661,8 @@ SUPPORTED_UCSC_GENOMES <- list(
FUN="standard_fetch_extended_ChromInfo_from_UCSC",
circ_seqs="chrM",
assembly_accession="GCF_000146045.2",
special_mappings=c(chrM="MT")
special_mappings=c(chrM="MT"),
get_Ensembl_seqlevels_from="chromAlias"
),

sacCer2=list(
Expand Down Expand Up @@ -616,6 +693,8 @@ fetchExtendedChromInfoFromUCSC <- function(genome,
unmapped_seqs=supported_genome$unmapped_seqs,
drop_unmapped=supported_genome$drop_unmapped,
goldenPath_url=goldenPath_url,
chromAliases=supported_genome$get_Ensembl_seqlevels_from,
duplicated_contigs=supported_genome$duplicated_contigs,
quiet=quiet)
}

12 changes: 12 additions & 0 deletions man/fetchExtendedChromInfoFromUCSC.Rd
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Original file line number Diff line number Diff line change
Expand Up @@ -102,6 +102,18 @@ fetchExtendedChromInfoFromUCSC(genome,
column, that is, \code{assembled-molecule}s first, then \code{alt-scaffold}s,
etc, and NAs last. Then within each group they are sorted by UCSC seqlevel
rank as determined by \code{\link{rankSeqlevels}()}.

If the UCSC Genome Browser provides tables to convert UCSC chromosome
names to Ensembl chromosome names, the returned data frame has 1
additional column:
\itemize{
\item \code{Ensembl_seqlevel}: Character vector. This information is
obtained from tables provided by UCSC Genome Browser (tables
chromAlias or ucscToEnsembl). It is merged with Ensembl chromosome
names provided by \code{genomeStyles}. It can contain NAs for missing
mapping between UCSC and Ensembl names. If all values are NA, then
column is not returned.
}
}

\note{
Expand Down