vignette/sets/gencode/gencode27/scripts/1_load_gencode.R

In momeara/data_repo: Load bioinformatics datasets into a local database

# -*- tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
# vi: set ts=2 noet:

library(plyr)
library(dplyr)
library(seqinr)
library(stringr)
library(BioChemPantry)

pantry <- get_pantry()
pantry %>% create_schema("gencode27")
pantry <- get_pantry("gencode27")

staging_directory <- get_staging_directory("gencode27")

system(paste0("
cd ", staging_directory, "
wget ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_27/gencode.v27.pc_translations.fa.gz
gunzip gencode.v27.pc_translations.fa.gz
mkdir dump/
mv gencode.v27.pc_translations.fa dump/
"))

protein_sequences <- seqinr::read.fasta(
	paste0(staging_directory, "/dump/gencode.v27.pc_translations.fa"),
	seqtype="AA",
	as.string=T) %>%
	plyr::adply(1, function(df){
		name <- df %>% attr("name") %>% stringr::str_split_fixed("[|]", 8)
		data_frame(
		ensembl_protein_id =  name[1],
		ensembl_transcript_id = name[2],
		ensembl_gene_id = name[3],
		hgnc_gene_symbol = name[7],
		entrez_id = as.integer(name[8]),
		sequence = as.character(df))
	}) %>%
	dplyr::select(-X1)


pantry %>% dplyr::copy_to(
	df=protein_sequences,
	name="protein_sequences",
	temporary=F,
	indexes=list(
		"ensembl_protein_id",
		"entrez_id"))