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Clean up style/formatting after merging of pull request #5. Bump vers…
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…ion.
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hpages committed Dec 20, 2019
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ Description: Contains data and functions that
sequence naming conventions (e.g., "chr1" versus "1"),
including a function that attempts to place sequence names in
their natural, rather than lexicographic, order.
Version: 1.23.0
Version: 1.23.1
Encoding: UTF-8
Author: Sonali Arora, Martin Morgan, Marc Carlson, H. Pagès
Maintainer: Bioconductor Package Maintainer <[email protected]>
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112 changes: 65 additions & 47 deletions R/fetchExtendedChromInfoFromUCSC.R
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
### Some low-level helpers.
###

fetch_table_from_UCSC <- function(genome, table="chromInfo", colnames,
.fetch_table_from_UCSC <- function(genome, table="chromInfo", colnames,
goldenPath_url="http://hgdownload.cse.ucsc.edu/goldenPath")
{
url <- paste(goldenPath_url, genome, "database", paste0(table, ".txt.gz"), sep="/")
Expand Down Expand Up @@ -180,41 +180,54 @@ fetch_GenBankAccn2seqlevel_from_NCBI <- function(assembly, AssemblyUnits=NULL)
ans
}

fetch_ensembl_chromNames_from_UCSC <- function(genome, chromAliases, UCSC_seqlevels, duplicated_contigs)
.fetch_Ensembl_seqlevels_from_UCSC <-
function(genome, Ensembl_mapping_tables, UCSC_seqlevels, duplicated_contigs,
goldenPath_url="http://hgdownload.cse.ucsc.edu/goldenPath")
{
stopifnot(identical(Ensembl_mapping_tables, "chromAlias") ||
identical(Ensembl_mapping_tables,
c("chromAlias", "ucscToEnsembl")))
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"])
## 1. Fill in what is already provided by the package GenomeInfoDb.
org <- suppressWarnings(mapGenomeBuilds(genome)[1L, "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$UCSC %in% names(ensembl_seqlevels),]
chroms <- chroms[chroms$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))]
## 2. Fetch info from UCSC.
for (tbl in Ensembl_mapping_tables) {
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")
} else {
## 'tbl' is "ucscToEnsembl"
colnames <- c("chrom", "alias")
}
chroms <- fetch_table_from_UCSC(genome, colnames=colnames, table=tbl)
chroms <- .fetch_table_from_UCSC(genome, tbl, colnames,
goldenPath_url=goldenPath_url)
if ("source" %in% colnames(chroms)) {
chroms <- chroms[grep("ensembl", chroms[,"source"]),c("chrom", "alias")]
idx <- grep("ensembl", chroms[ , "source"])
chroms <- chroms[idx, 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"]
idx <- which(!(chroms[ , "alias"] %in% duplicated_contigs))
chroms <- chroms[idx, ]
rownames(chroms) <- chroms[ , "chrom"]
keep_me <- uscs_seqlevels_without_ensembl %in% rownames(chroms)
uscs_seqlevels_without_ensembl <-
uscs_seqlevels_without_ensembl[keep_me]
ensembl_seqlevels[uscs_seqlevels_without_ensembl] <-
chroms[uscs_seqlevels_without_ensembl, "alias"]
}
}
as.character(ensembl_seqlevels)
Expand All @@ -228,15 +241,15 @@ standard_fetch_extended_ChromInfo_from_UCSC <- function(
special_mappings,
unmapped_seqs,
drop_unmapped,
goldenPath_url,
chromAliases,
Ensembl_mapping_tables,
duplicated_contigs,
goldenPath_url,
quiet)
{
chrominfo <- fetch_table_from_UCSC(genome,
table="chromInfo",
colnames=c("chrom", "size", "fileName"),
goldenPath_url=goldenPath_url)
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)
if (any(is.na(circular_idx)))
Expand Down Expand Up @@ -330,12 +343,18 @@ 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$UCSC_seqlevel,
duplicated_contigs=duplicated_contigs)
if (!all(is.na(Ensembl_seqlevel)))
ans <- cbind(ans, Ensembl_seqlevel, stringsAsFactors=FALSE)
if (!is.null(Ensembl_mapping_tables)) {
## Add mapping to ensembl chromosomes from UCSC tables.
Ensembl_seqlevel <- .fetch_Ensembl_seqlevels_from_UCSC(
genome,
Ensembl_mapping_tables,
ans$UCSC_seqlevel,
duplicated_contigs,
goldenPath_url=goldenPath_url)
if (!all(is.na(Ensembl_seqlevel)))
ans <- cbind(ans, Ensembl_seqlevel=Ensembl_seqlevel,
stringsAsFactors=FALSE)
}
rownames(ans) <- NULL
ans
}
Expand All @@ -350,7 +369,7 @@ SUPPORTED_UCSC_GENOMES <- list(
circ_seqs="chrM",
assembly_accession="GCF_000001405.26",
special_mappings=c(chrM="MT"),
get_Ensembl_seqlevels_from=c("chromAlias","ucscToEnsembl"),
Ensembl_mapping_tables=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 @@ -372,7 +391,7 @@ SUPPORTED_UCSC_GENOMES <- list(
chr6_ssto_hap7="HSCHR6_MHC_SSTO_CTG1",
chr17_ctg5_hap1="HSCHR17_1_CTG5"),
unmapped_seqs=list(`assembled-molecule`="chrM"),
get_Ensembl_seqlevels_from=c("chromAlias","ucscToEnsembl")
Ensembl_mapping_tables=c("chromAlias", "ucscToEnsembl")
),

hg18=list(
Expand All @@ -386,7 +405,6 @@ 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
Expand All @@ -395,7 +413,7 @@ SUPPORTED_UCSC_GENOMES <- list(
circ_seqs="chrM",
assembly_accession="GCF_000001515.5",
special_mappings=c(chrM="MT"),
get_Ensembl_seqlevels_from=c("chromAlias","ucscToEnsembl")
Ensembl_mapping_tables=c("chromAlias", "ucscToEnsembl")
),

panTro3=list(
Expand All @@ -422,7 +440,7 @@ SUPPORTED_UCSC_GENOMES <- list(
circ_seqs="chrM",
assembly_accession="GCF_000003055.5",
special_mappings=c(chrM="MT"),
get_Ensembl_seqlevels_from="chromAlias"
Ensembl_mapping_tables="chromAlias"
),

bosTau7=list(
Expand All @@ -437,7 +455,7 @@ SUPPORTED_UCSC_GENOMES <- list(
circ_seqs="chrM",
assembly_accession="GCF_000003055.4",
special_mappings=c(chrM="MT"),
get_Ensembl_seqlevels_from=c("chromAlias","ucscToEnsembl")
Ensembl_mapping_tables=c("chromAlias", "ucscToEnsembl")
),

### Dog
Expand All @@ -449,7 +467,7 @@ SUPPORTED_UCSC_GENOMES <- list(
chr4="chr04", chr5="chr05", chr6="chr06",
chr7="chr07", chr8="chr08", chr9="chr09",
chrM="MT"),
get_Ensembl_seqlevels_from="chromAlias"
Ensembl_mapping_tables="chromAlias"
),

canFam2=list(
Expand All @@ -466,7 +484,7 @@ SUPPORTED_UCSC_GENOMES <- list(
musFur1=list(
FUN="standard_fetch_extended_ChromInfo_from_UCSC",
assembly_accession="GCF_000215625.1",
get_Ensembl_seqlevels_from="chromAlias"
Ensembl_mapping_tables="chromAlias"
),

### Mouse
Expand All @@ -476,7 +494,7 @@ SUPPORTED_UCSC_GENOMES <- list(
assembly_accession="GCF_000001635.20",
AssemblyUnits=c("C57BL/6J", "non-nuclear"),
special_mappings=c(chrM="MT"),
get_Ensembl_seqlevels_from=c("chromAlias","ucscToEnsembl")
Ensembl_mapping_tables=c("chromAlias", "ucscToEnsembl")
),

mm9=list(
Expand Down Expand Up @@ -507,7 +525,7 @@ SUPPORTED_UCSC_GENOMES <- list(
circ_seqs="chrM",
assembly_accession="GCF_000003025.5",
special_mappings=c(chrM="MT"),
get_Ensembl_seqlevels_from="chromAlias"
Ensembl_mapping_tables="chromAlias"
),

susScr2=list(
Expand All @@ -523,10 +541,10 @@ SUPPORTED_UCSC_GENOMES <- list(
circ_seqs="chrM",
assembly_accession="GCF_000001895.5",
special_mappings=c(chrM="MT"),
get_Ensembl_seqlevels_from="chromAlias"
Ensembl_mapping_tables="chromAlias"
## https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/rn6.txt
## LINES 856:864
, duplicated_contigs=c("AABR07023006.1","AABR07022518.1")
, duplicated_contigs=c("AABR07023006.1", "AABR07022518.1")
),

### Rhesus
Expand All @@ -551,7 +569,7 @@ SUPPORTED_UCSC_GENOMES <- list(
special_mappings=c(chrLGE22C19W28_E50C23="ChrE22C19W28_E50C23",
chrLGE64="ChrE64",
chrM="MT"),
get_Ensembl_seqlevels_from=c("chromAlias","ucscToEnsembl")
Ensembl_mapping_tables=c("chromAlias", "ucscToEnsembl")
),

galGal3=list(
Expand All @@ -572,7 +590,7 @@ SUPPORTED_UCSC_GENOMES <- list(
FUN="standard_fetch_extended_ChromInfo_from_UCSC",
circ_seqs="chrM",
#assembly_accession="GCA_000180675.1"
get_Ensembl_seqlevels_from="chromAlias"
Ensembl_mapping_tables="chromAlias"
),

### Zebra finch
Expand All @@ -596,7 +614,7 @@ SUPPORTED_UCSC_GENOMES <- list(
circ_seqs="chrM",
assembly_accession="GCF_000002035.4",
special_mappings=c(chrM="MT"),
get_Ensembl_seqlevels_from="chromAlias"
Ensembl_mapping_tables="chromAlias"
),

#Too messy!
Expand All @@ -622,7 +640,7 @@ SUPPORTED_UCSC_GENOMES <- list(
assembly_accession="GCF_000001215.4",
## special_mappings=c(chrM="MT"),
special_mappings=c(chrM="mitochondrion_genome"),
get_Ensembl_seqlevels_from="chromAlias"
Ensembl_mapping_tables="chromAlias"
),

dm3=list(
Expand Down Expand Up @@ -662,7 +680,7 @@ SUPPORTED_UCSC_GENOMES <- list(
circ_seqs="chrM",
assembly_accession="GCF_000146045.2",
special_mappings=c(chrM="MT"),
get_Ensembl_seqlevels_from="chromAlias"
Ensembl_mapping_tables="chromAlias"
),

sacCer2=list(
Expand Down Expand Up @@ -692,9 +710,9 @@ fetchExtendedChromInfoFromUCSC <- function(genome,
special_mappings=supported_genome$special_mappings,
unmapped_seqs=supported_genome$unmapped_seqs,
drop_unmapped=supported_genome$drop_unmapped,
goldenPath_url=goldenPath_url,
chromAliases=supported_genome$get_Ensembl_seqlevels_from,
Ensembl_mapping_tables=supported_genome$Ensembl_mapping_tables,
duplicated_contigs=supported_genome$duplicated_contigs,
goldenPath_url=goldenPath_url,
quiet=quiet)
}

10 changes: 5 additions & 5 deletions man/fetchExtendedChromInfoFromUCSC.Rd
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Original file line number Diff line number Diff line change
Expand Up @@ -108,11 +108,11 @@ fetchExtendedChromInfoFromUCSC(genome,
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.
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.
}
}

Expand Down

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