In meekrob/ParasiteXML: Functions For Converting Parasite Database XML into R Code

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(ParasiteXML)
suppressPackageStartupMessages(library(biomaRt))
suppressPackageStartupMessages(library(GenomicRanges))

QUERY='<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query  virtualSchemaName = "parasite_mart" formatter = "TSV" header = "0" uniqueRows = "0" count = "" datasetConfigVersion = "0.6" >

    <Dataset name = "wbps_gene" interface = "default" >
        <Filter name = "gene_name" value = "ELT-2,ACT-1,erfa-3"/>
        <Filter name = "biotype" value = "protein_coding"/>
        <Filter name = "species_id_1010" value = "caelegprjna13758"/>
        <Attribute name = "wbps_gene_id" />
        <Attribute name = "external_gene_id" />
        <Attribute name = "chromosome_name" />
        <Attribute name = "start_position" />
        <Attribute name = "end_position" />
        <Attribute name = "strand" />
    </Dataset>
</Query>'

library(ParasiteXML)
library(biomaRt)
R_query = format_BM_from_XML(QUERY)

if(!exists("mart")) {mart = getParamart()}
genes = runWithMart(R_query, mart)
genes$chromosome_name = paste("chr",genes$chromosome_name, sep='')
genes$strand = ifelse(genes$strand==1, '+', '-')

library(GenomicRanges)
#grGenes = makeGRangesFromMartDataFrame(genes)