grimbough

    fullXmlQuery <- "<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE Query>
        <Query  virtualSchemaName = 'default' uniqueRows = '1' count = '0' datasetConfigVersion = '0.6' header='1' requestid= 'biomaRt'>
            <Dataset name = 'hsapiens_gene_ensembl'>
                <Attribute name = 'phenotype_description'/>
                <Attribute name = 'ensembl_gene_id'/>
                <Filter name = 'ensembl_gene_id' value = 'ENSG00000094804'/>
            </Dataset>
        </Query>"

    rcurl_return <- RCurl::postForm(uri = "http://www.ensembl.org:80/biomart/martservice?", 

grimbough

fullXmlQuery <- "<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE Query>
        <Query  virtualSchemaName = 'default' uniqueRows = '1' count = '0' datasetConfigVersion = '0.6' header='1' requestid= 'biomaRt'>
            <Dataset name = 'hsapiens_gene_ensembl'>
                <Attribute name = 'ensembl_transcript_id'/>
                <Attribute name = 'ensembl_exon_id'/>
                <Attribute name = 'rank'/>
                <Attribute name = 'genomic_coding_start'/>
                <Attribute name = 'cds_start'/>
                <Attribute name = '5_utr_start'/>
            </Dataset>

grimbough

library(ShortRead)

## create a single string with the number of characters defined by 'length'
## and the letter sampled from 'alphabet'
generateString <- function(length = 50, alphabet = c("A","C","G","T") ) { 
    paste0(sample(alphabet, size = length, replace = TRUE), collapse = "") 
}

## create a ShortReadQ object containing 'nreads' reads, each of which has length 'length'
createFastq <- function(nreads, length) {