The tritrypdb just released a new version. Let us make new annotation data from it.
## These functions take _forever_ the first time around.
lm_annot <- make_eupath_organismdbi(species="Leishmania major", reinstall=TRUE)In order to load these new packages, I rather need to remember their names… Happily I have a function for that.
lm_name <- get_eupath_pkgnames("Leishmania major")
lm_name$organismdbiFor those packages I have generated/installed, use this to generate an annotation table. Oh, but I prefixed the column names with ‘annot_’ in order to make sure that nothing is duplicated with the GO tables, ortholog tables, etc. As a result, these are wrong until the new annotations are loaded.
## Just to save on typing
lm_db <- get0(lm_name$orgdb)
lm_db
wanted_fields <- c("annot_gene_location_text",
"annot_cds_length",
"annot_gene_name",
"annot_gene_product",
"annot_gene_type",
"annot_strand",
"annot_gene_entrez_id",
"annot_gene_orthomcl_name")
lm_annot <- load_orgdb_annotations(lm_db,
keytype="gid",
fields=wanted_fields)
lm_annot <- extract_gene_locations(lm_annot$genes)lm_gff_file <- "reference/TriTrypDB-37_LmajorFriedlin.gff"
lm_gff_annotations <- sm(load_gff_annotations(lm_gff_file, type="exon"))if (!isTRUE(get0("skip_load"))) {
pander::pander(sessionInfo())
message(paste0("This is hpgltools commit: ", get_git_commit()))
message(paste0("Saving to ", savefile))
tmp <- sm(saveme(filename=savefile))
}## If you wish to reproduce this exact build of hpgltools, invoke the following:## > git clone http://github.com/abelew/hpgltools.git## > git reset cab8817432ec3a0a81e7922677332f023341b9dd## R> packrat::restore()## This is hpgltools commit: Thu Jul 12 11:17:53 2018 -0400: cab8817432ec3a0a81e7922677332f023341b9dd## Saving to 01_annotation_v20180501.rda.xz