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#TxDbLite

TxDbLite is a minimalist annotation package generator, designed to extract annotations from FASTA files. It relies upon some R/Bioconductor infrastructure packages and a few filthy tricks. To install it, do the following in R:

source("http://bioconductor.org/biocLite.R")
biocLite("devtools")
biocLite("ramsinghlab/TxDbLite")

The underlying assumption is that users want to quantify transcript-level RNA expression, may or may not have a GTF file for each transcriptome, and would like to extract as much information as possible about the transcripts from what they do have. This in turn allows the arkas package to automatically determine what transcriptomes a dataset came from, whether those are already known to the package, and how to generate certain types of annotation for specific transcriptomes from Ensembl, RepBase, and ERCC (spike-in controls from Ambion). It turns out that in some cases, biomaRt will not perform the mappings that a user might expect, so we try to take care of that issue here.

The user presumably already has the fasta file in question; typically the TxDbLite package will be automatically invoked during the creation of a new Kallisto index. If a fasta file "smells like" a recognizable class of transcripts, and the user does not already appear to have installed or created annotations for the transcriptome, arkas will then attempt to do so. This can also be performed manually. The below example takes a recent Ensembl build for Drosophila melanogaster (the fruit fly) and processes it. The FASTA file used in the example is
ftp://ftp.ensembl.org/pub/release-81/fasta/drosophila_melanogaster/ncrna/Drosophila_melanogaster.BDGP6.ncrna.fa.gz and should be downloaded into your working directory. Alternatively, a copy of it resides in inst/extdata/.

fasta <- "Drosophila_melanogaster.BDGP6.ncrna.fa.gz"
ensdb <- ensDbLiteFromFasta(fasta)
show(EnsDbLite(ensdb))

EnsDbLite :
|package_name: EnsDbLite.Drosophila_melanogaster.BDGP6.ncrna
|db_type: EnsDbLite
|type_of_gene_id: Ensembl Gene ID
|created_by: TxDbLite 1.9.16
|creation_time: Sun Aug 30 15:48:41 2015
|organism: Dmelanogaster
|genome_build: ncrna
|source_file: Drosophila_melanogaster.BDGP6.ncrna.fa.gz
| 4098 transcripts from 3384 bundles (genes).