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comparison test-data/test.r @ 0:0a0bba8e1823 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq commit 8b472e8680bb0ae5d11ee48b642ab305f9333a48
author rnateam
date Wed, 22 Feb 2017 07:32:08 -0500
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-1:000000000000 0:0a0bba8e1823
1 library(NASTIseq)
2
3 ## generation of test set
4 # data(WholeRoot)
5 # WholeRoot$genepos$feature <- 'gene'
6 #
7 # set_attri <- function(attri){
8 # attri = paste('gene_id ', '"', attri, '"', ';', sep = '')
9 # return(attri)
10 # }
11 #
12 # WholeRoot$genepos$attributes = as.character(lapply(as.character(WholeRoot$genepos$attributes), set_attri))
13 #
14 # write.table(WholeRoot$genepos, file = "input_TAIR10_annotation.gtf", row.names = FALSE, col.names = FALSE, sep = "\t", quote = FALSE)
15 # write.table(WholeRoot$smat, file = "input_read_count_smt.tsv", col.names = FALSE, sep = "\t", quote = FALSE)
16 # write.table(WholeRoot$asmat, file = "input_read_count_asmt.tsv", col.names = FALSE, sep = "\t", quote = FALSE)
17 #
18 # write.table(WholeRoot$pospairs, file = "input_positive_pair.tsv", row.names = FALSE, col.names = FALSE, sep = "\t", quote = FALSE)
19
20 genepos = read.delim("input_TAIR10_annotation.gtf", header=FALSE, comment.char="#")
21 colnames(genepos) = c("seqname", "source", "feature", "start", "end", "score", "strand", "frame", "attributes")
22 genepos = subset(genepos, feature=="gene")
23
24 get_id = function(attri){
25 gene_info = strsplit(attri, ";")[[1]][1]
26 gene_id = strsplit(gene_info, " ")[[1]][2]
27 gene_id = gsub("\"", "", gene_id)
28 return(gene_id)
29 }
30
31 genepos$attributes = as.character(lapply(as.character(genepos$attributes), get_id))
32
33 pospairs = read.table("input_positive_pair.tsv", sep = "\t", as.is = TRUE)
34
35 smat = as.matrix(read.table("input_read_count_smt.tsv", sep = "\t", row.names = 1))
36
37 asmat = as.matrix(read.table("input_read_count_asmt.tsv", sep = "\t", row.names = 1))
38
39 WRscore = getNASTIscore(smat, asmat)
40
41 negpairs = getnegativepairs(genepos)
42
43 WRpred = NASTIpredict(smat,asmat, pospairs, negpairs)
44
45 WRpred_rocr = prediction(WRpred$predictions,WRpred$labels)
46
47 thr = defineFDR(WRpred_rocr,0.05)
48
49 WR_names = FindNATs(WRscore, thr, pospairs, genepos)
50
51 write.table(WR_names$newpairs, file = "output_newpairs.tsv", row.names = FALSE, col.names = FALSE, sep = "\t", quote = FALSE)
52
53 write.table(WR_names$neworphan, file = "output_neworphan.tsv", row.names = FALSE, col.names = FALSE, sep = "\t", quote = FALSE)