Mercurial > repos > mvdbeek > r_goseq_1_22_0
comparison get_length_and_gc_content.r @ 10:7f8d888e3355 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
author | mvdbeek |
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date | Thu, 25 Feb 2016 06:18:47 -0500 |
parents | 15ce6435ab83 |
children | 02e88556ce1d |
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9:d1eed994287a | 10:7f8d888e3355 |
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15 parser <- OptionParser(usage = "%prog [options] file", option_list=option_list) | 15 parser <- OptionParser(usage = "%prog [options] file", option_list=option_list) |
16 args = parse_args(parser) | 16 args = parse_args(parser) |
17 | 17 |
18 GTFfile = args$gtf | 18 GTFfile = args$gtf |
19 FASTAfile = args$fasta | 19 FASTAfile = args$fasta |
20 output = args$output | 20 output_file = args$output |
21 | 21 |
22 #Load the annotation and reduce it | 22 #Load the annotation and reduce it |
23 GTF <- import.gff(GTFfile, format="gtf", genome=NA, feature.type="exon") | 23 GTF <- import.gff(GTFfile, format="gtf", genome=NA, feature.type="exon") |
24 grl <- reduce(split(GTF, elementMetadata(GTF)$gene_id)) | 24 grl <- reduce(split(GTF, elementMetadata(GTF)$gene_id)) |
25 reducedGTF <- unlist(grl, use.names=T) | 25 reducedGTF <- unlist(grl, use.names=T) |
40 c(width, nGCs/width) | 40 c(width, nGCs/width) |
41 } | 41 } |
42 output <- t(sapply(split(reducedGTF, elementMetadata(reducedGTF)$gene_id), calc_GC_length)) | 42 output <- t(sapply(split(reducedGTF, elementMetadata(reducedGTF)$gene_id), calc_GC_length)) |
43 colnames(output) <- c("Length", "GC") | 43 colnames(output) <- c("Length", "GC") |
44 | 44 |
45 write.table(output, file="GC_lengths.tsv", sep="\t") | 45 write.table(output, file=output_file, sep="\t") |