M.tuberculosis 2018 proteomics: Collecting annotation data.

1 Annotation version: 20180215

1.1 Genome annotation input

1.1.1 Read a gff file

In contrast, it is possible to load most annotations of interest directly from the gff files used in the alignments. More in-depth information for the human transcriptome may be extracted from biomart.

## The old way of getting genome/annotation data
mtb_gff <- "reference/mycobacterium_tuberculosis_h37rv_2.gff.gz"

mtb_genome <- "reference/mtuberculosis_h37rv_genbank.fasta"
mtb_cds <- "reference/mtb_cds.fasta"

mtb_annotations <- sm(load_gff_annotations(mtb_gff, type="gene"))
rownames(mtb_annotations) <- mtb_annotations[["ID"]]

1.1.2 Download from microbesonline

## First figure out the ID for the Mtb genome:
ids <- get_microbesonline_ids("37")
head(ids)
## Mycobacterium tuberculosis H37Rv is the first entry and has id: 83332
mtb_microbes <- load_microbesonline_annotations(ids=83332)

## I made a nifty function to do this stuff: load_uniprotws_annotations().
## It is slow, though.
mtb_uniprot_annot <- load_uniprotws_annotations()

1.2 Getting ontology data

mtb_go <- load_microbesonline_go(id=83332)

if (!isTRUE(get0("skip_load"))) {
  pander::pander(sessionInfo())
  message(paste0("This is hpgltools commit: ", get_git_commit()))
  this_save <- paste0(gsub(pattern="\\.Rmd", replace="", x=rmd_file), "-v", ver, ".rda.xz")
  message(paste0("Saving to ", this_save))
  tmp <- sm(saveme(filename=this_save))
}

## If you wish to reproduce this exact build of hpgltools, invoke the following:

## > git clone http://github.com/abelew/hpgltools.git

## > git reset 7de4503f6bb5724c28cce24af5dbee22bb1c0cae

## R> packrat::restore()

## This is hpgltools commit: Thu Apr 12 22:08:53 2018 -0400: 7de4503f6bb5724c28cce24af5dbee22bb1c0cae

## Saving to 01_annotation-v20180215.rda.xz