I think I finally worked out all(most?) of the kinks in the processing of DIA data. Thus I want to have a fresh run of all the tasks required to interpret the results.
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"))
colnames(mtb_annotations) <- gsub(pattern="\\.", replacement="", x=colnames(mtb_annotations))
mtb_annotations[["description"]] <- gsub(pattern="\\+", replacement=" ",
x=mtb_annotations[["description"]])
mtb_annotations[["function"]] <- gsub(pattern="\\+", replacement=" ",
x=mtb_annotations[["function"]])
rownames(mtb_annotations) <- mtb_annotations[["ID"]]Apparently I queried the microbesonline too often and now I get an error whenever I try to use them, this disappoints me.
## 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## I made a nifty function to do this stuff: load_uniprotws_annotations().
## It is slow, though.
mtb_microbes <- load_microbesonline_annotations(id=83332)## The species being downloaded is: Mycobacterium tuberculosis H37Rv## mtb_uniprot_annot <- load_uniprotws_annotations()
mtb_uniprot_annot <- load_uniprot_annotations(file="reference/uniprot_3AUP000001584.txt.gz")##
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|=================================================================| 100%## Finished parsing, creating data frame.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 0b63ce6abcbb822832fe4631b4916f94931d8648## R> packrat::restore()## This is hpgltools commit: Wed Sep 5 12:04:45 2018 -0400: 0b63ce6abcbb822832fe4631b4916f94931d8648## Saving to 01_annotation_20180817-v20180817.rda.xz