--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.r	Wed Feb 22 07:32:08 2017 -0500
@@ -0,0 +1,53 @@
+library(NASTIseq)
+
+## generation of test set
+# data(WholeRoot)
+# WholeRoot$genepos$feature <- 'gene'
+#
+# set_attri <- function(attri){
+#   attri = paste('gene_id ', '"', attri, '"', ';', sep = '')
+#   return(attri)
+# }
+#
+# WholeRoot$genepos$attributes = as.character(lapply(as.character(WholeRoot$genepos$attributes), set_attri))
+#
+# write.table(WholeRoot$genepos, file = "input_TAIR10_annotation.gtf", row.names = FALSE,  col.names = FALSE,  sep = "\t",  quote = FALSE)
+# write.table(WholeRoot$smat, file = "input_read_count_smt.tsv",  col.names = FALSE,  sep = "\t", quote = FALSE)
+# write.table(WholeRoot$asmat, file = "input_read_count_asmt.tsv", col.names = FALSE, sep = "\t", quote = FALSE)
+#
+# write.table(WholeRoot$pospairs, file = "input_positive_pair.tsv", row.names = FALSE, col.names = FALSE, sep = "\t", quote = FALSE)
+
+genepos = read.delim("input_TAIR10_annotation.gtf", header=FALSE, comment.char="#")
+colnames(genepos) = c("seqname", "source", "feature", "start", "end", "score", "strand", "frame", "attributes")
+genepos = subset(genepos, feature=="gene")
+
+get_id = function(attri){
+  gene_info = strsplit(attri, ";")[[1]][1]
+  gene_id = strsplit(gene_info, " ")[[1]][2]
+  gene_id = gsub("\"", "", gene_id)
+  return(gene_id)
+}
+
+genepos$attributes = as.character(lapply(as.character(genepos$attributes), get_id))
+
+pospairs = read.table("input_positive_pair.tsv", sep = "\t", as.is = TRUE)
+
+smat = as.matrix(read.table("input_read_count_smt.tsv",  sep = "\t",  row.names = 1))
+
+asmat = as.matrix(read.table("input_read_count_asmt.tsv",  sep = "\t",  row.names = 1))
+
+WRscore = getNASTIscore(smat, asmat)
+
+negpairs = getnegativepairs(genepos)
+
+WRpred = NASTIpredict(smat,asmat, pospairs, negpairs)
+
+WRpred_rocr = prediction(WRpred$predictions,WRpred$labels)
+
+thr = defineFDR(WRpred_rocr,0.05)
+
+WR_names = FindNATs(WRscore, thr, pospairs, genepos)
+
+write.table(WR_names$newpairs, file = "output_newpairs.tsv", row.names = FALSE, col.names = FALSE, sep = "\t", quote = FALSE)
+
+write.table(WR_names$neworphan, file = "output_neworphan.tsv", row.names = FALSE, col.names = FALSE, sep = "\t", quote = FALSE)