Build a misha genome database from a name

Builds a misha genomic database for a named assembly. Resolves the name through the registry chain (or pattern-fallback for GC[FA]_* accessions), downloads the FASTA, calls gdb.create to build the seq-only groot, then dispatches to gdb.install_intervals for the requested sets.

Usage

gdb.build_genome(
  name,
  path = name,
  registry = NULL,
  sets = c("genes", "rmsk", "cgi", "cytoband"),
  prefix = "",
  gene_sets = c(tss = "tss", exons = "exons", utr3 = "utr3", utr5 = "utr5"),
  gtf_priority = c("ncbiRefSeq", "bestRefSeq", "ensGene", "augustus", "xenoRefGene"),
  chrom_naming = NULL,
  target_chroms = NULL,
  target_lengths = NULL,
  min_coverage = 1,
  match_by_length = TRUE,
  format = NULL,
  verbose = TRUE
)

Arguments

name

Genome name (registry key, alias, or GC[FA]_* accession).

path

Output directory; must not exist.

registry

Optional path to an explicit registry YAML.

sets

Subset of c("genes", "rmsk", "cgi", "cytoband"). Empty vector character(0) = sequence-only build.

prefix

Character scalar prepended to set names (see gdb.install_intervals).

gene_sets

Named character vector mapping the four gintervals.import_genes() roles to on-disk set names; NA skips a role.

gtf_priority

Character vector ordering GTF source preference.

chrom_naming

Optional override for the recipe's chrom_naming. Selects which name space the canonical chrom names should come from. For ucsc-hub: any chromAlias column ("ucsc", "genbank", "refseq", "ncbi"), plus the friendly aliases "sequence_name" (= "assembly") and "accession" (keep the FASTA's source column). For ncbi: "sequence_name" (default), "ucsc", or "accession". NULL (default) keeps whatever the recipe specifies.

target_chroms

Optional character vector of chrom names the resulting groot should align to (typically the output of halStats --sequenceStats, the chrom names in a HAL file you intend to liftover against). When supplied, misha auto-picks the chromAlias column whose values cover target_chroms best and uses that column as the canonical naming, instead of chrom_naming. Honored only by the ucsc-hub backend; supplying it with any other source is an error (raised before any download).

target_lengths

Optional numeric vector aligned with target_chroms (typically the second field of halStats --sequenceStats). When supplied alongside target_chroms and with match_by_length = TRUE, this is the strong-guarantee path: misha force-aligns the hub FASTA to target_chroms, placing every target on its chromAlias row by name match across columns or unique-on-both-sides length pairing. If any target can't be placed, the build errors (in the pre-flight, before the multi-GB FASTA download). On success the resulting groot's chrom names are exactly target_chroms (alias rows not in target_chroms keep their original FASTA-header accession). Honored only by the ucsc-hub backend.

min_coverage

Minimum fraction of groot chroms that must appear in a chromAlias column for that column to be picked as canonical (forwarded to gdb.install_intervals). Default 1.0 (strict). Lower to e.g. 0.99 when a column has small gaps – typical when a target column doesn't span every contig (e.g. UCSC's genbank column has no value for the mitochondrion in many hubs, leaving 1 stray chrom). Honored only by the ucsc-hub backend; supplying a non-default value for any other source is an error (raised before any download).

match_by_length

Forwarded to gdb.install_intervals. When TRUE (default), complements column-based canonical detection with a per-row length match for alias rows the chosen column couldn't cover, and switches asset translation to a cross-column per-row lookup so GFFs in any naming scheme import cleanly. Set FALSE for the stricter single-column-only behavior.

format

"indexed" or "per-chromosome"; NULL => getOption("gmulticontig.indexed_format", TRUE).

verbose

If TRUE, prints progress.

Value

None (invisible NULL). The installed gene-derived sets (tss, exons, utr3, utr5) carry a name column (transcript/RNA accession) and a geneName column (gene symbol from the source annotation; blank when the source has no symbol).

Details

For details on resolution, sources, sets, and chromosome-alias handling, see gdb.install_intervals.

See also

gdb.install_intervals, gdb.create, gdb.list_genomes, gdb.genome_info.

Examples

if (FALSE) { # \dontrun{
gdb.build_genome("hg38", path = "~/genomes/hg38")
gdb.build_genome("GCA_004023825.1",
    path   = "~/genomes/arctic_fox",
    prefix = "intervs.global."
)
# Match HAL/Cactus canonical names (GenBank accessions like JH880237.1):
gdb.build_genome("GCF_000298355.1",
    path         = "~/genomes/Bos_mutus",
    chrom_naming = "genbank",
    prefix       = "intervs.global."
)
} # }