# this file helps extract information from ensembl with gene name as input

# 11/02/2018, pxy7896

library(biomaRt)

# 使用参数

# args=commandArgs(T)

# 从文件读取

geneNamesFile <- "geneNames.txt"

otherInfoFile <- "otherInfo.txt"

raw <- read.table(geneNamesFile, col.names = c("geneNames"), stringsAsFactors = FALSE)

# geneNames is character

geneNames <- raw[["geneNames"]]

#geneNames <- args[1]

otherInfo <- read.table(otherInfoFile, stringsAsFactors = FALSE)

dataSet <- otherInfo[[1]][1]

# choose database

#dataSet <- args[2]

mart = useMart("ensembl", dataset=dataSet)

attr <- c("hgnc_symbol", "ensembl_transcript_id", "chromosome_name", "transcript_start", "transcript_end")

# get transcript ids

ids <- getBM(attributes = attr, filters = "hgnc_symbol", values = geneNames, mart = mart)

write.table(ids, "ids.txt", sep="\t", quote=FALSE, row.names=FALSE)

targetIds <- ids["ensembl_transcript_id"]

# get exons info

exonAttr <- c("5_utr_start","5_utr_end","3_utr_start","3_utr_end","strand", "ensembl_transcript_id", "ensembl_exon_id", "exon_chrom_start", "exon_chrom_end")

#attr2 <- c(attr, exonAttr)

result <- getBM(attributes = exonAttr, filters = "ensembl_transcript_id", values = targetIds, mart = mart)

write.table(result, args[4], sep = "\t", quote = FALSE, row.names=FALSE)