Mercurial > repos > iuc > length_and_gc_content

annotate get_length_and_gc_content.r @ 2:e3ba567abdf5 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content commit 7b6b07d22f3e6fed77b2c237de2b0d96fa939711"
author iuc
date Fri, 11 Mar 2022 14:08:11 +0000
parents f088370d2a3c
children
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2ca1baabdae0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
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1 # originally by Devon Ryan, https://www.biostars.org/p/84467/
2ca1baabdae0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
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3 options(show.error.messages = F,
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4 error = function() {
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5 cat(geterrmessage(), file = stderr())
e3ba567abdf5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content commit 7b6b07d22f3e6fed77b2c237de2b0d96fa939711"
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6 q("no", 1, F)
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7 })
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2ca1baabdae0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
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9 # we need that to not crash galaxy with an UTF8 error on German LC settings.
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10 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
2ca1baabdae0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
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2ca1baabdae0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
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12 suppressPackageStartupMessages({
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13 library("GenomicRanges")
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14 library("rtracklayer")
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15 library("Rsamtools")
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16 library("optparse")
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17 library("data.table")
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18 })
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20 option_list <- list(
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21 make_option(c("-g", "--gtf"), type = "character",
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22 help = "Input gtf file with gene / exon information."),
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23 make_option(c("-f", "--fasta"), type = "character", default = NULL,
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24 help = "fasta file that corresponds to the supplied gtf."),
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25 make_option(c("-l", "--length"), type = "character", default = NULL,
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26 help = "Output file with Gene ID and length."),
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27 make_option(c("-c", "--gc_content"), type = "character", default = NULL,
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28 help = "Output file with Gene ID and GC content.")
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29 )
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2ca1baabdae0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
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31 parser <- OptionParser(usage = "%prog [options] file",
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32 option_list = option_list)
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33 args <- parse_args(parser)
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34
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35 gtf_file <- args$gtf
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36 fasta_file <- args$fasta
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37 length <- args$length
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38 gc_content <- args$gc_content
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40 # Check args:
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41 if (is.null(fasta_file) & !is.null(gc_content)) {
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42 stop("gc_content output requires fasta input")
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43 }
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44 if (is.null(length) & is.null(gc_content)) {
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45 stop("neither gc_content nor length was set nothing to do.")
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46 }
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47
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48 #Load the annotation and reduce it
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49 gtf <- import.gff(gtf_file, format = "gtf", genome = NA, feature.type = "exon")
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50 grl <- reduce(split(gtf, elementMetadata(gtf)$gene_id))
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51 reduced_gtf <- unlist(grl, use.names = T)
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52 elementMetadata(reduced_gtf)$gene_id <- rep(names(grl), elementNROWS(grl))
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53
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54 if (! is.null(gc_content)) {
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55 #Open the fasta file
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56 fasta <- FaFile(fasta_file)
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57 open(fasta)
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58
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59 #Add the GC numbers
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60 elementMetadata(reduced_gtf)$n_gcs <-
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61 letterFrequency(getSeq(fasta, reduced_gtf), "GC")[, 1]
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62 }
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63 elementMetadata(reduced_gtf)$widths <- width(reduced_gtf)
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65 #Create a list of the ensembl_id/GC/length
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66 if (! is.null(gc_content)) {
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67 calc_gc_length <- function(x) {
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68 n_gcs <- sum(elementMetadata(x)$n_gcs)
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69 width <- sum(elementMetadata(x)$widths)
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70 c(width, n_gcs / width)
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71 }
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72 output <- t(sapply(split(reduced_gtf, elementMetadata(reduced_gtf)$gene_id),
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73 calc_gc_length))
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74 output <- data.frame(setDT(data.frame(output), keep.rownames = TRUE)[])
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75 write.table(output[, c(1, 3)], file = gc_content,
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76 col.names = FALSE, row.names = FALSE,
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77 quote = FALSE, sep = "\t")
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78 } else {
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79 all_widths <- sapply(split(reduced_gtf, elementMetadata(reduced_gtf)$gene_id),
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80 function(x) {
e3ba567abdf5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content commit 7b6b07d22f3e6fed77b2c237de2b0d96fa939711"
iuc
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diff changeset
81 sum(elementMetadata(x)$widths)
e3ba567abdf5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content commit 7b6b07d22f3e6fed77b2c237de2b0d96fa939711"
iuc
parents: 1
diff changeset
82 })
e3ba567abdf5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content commit 7b6b07d22f3e6fed77b2c237de2b0d96fa939711"
iuc
parents: 1
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83 output <- data.frame(gene_id = names(all_widths),
e3ba567abdf5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content commit 7b6b07d22f3e6fed77b2c237de2b0d96fa939711"
iuc
parents: 1
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84 length = all_widths)
0
2ca1baabdae0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
diff changeset
85 }
2ca1baabdae0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
diff changeset
86
2
e3ba567abdf5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content commit 7b6b07d22f3e6fed77b2c237de2b0d96fa939711"
iuc
parents: 1
diff changeset
87 if (! is.null(length)) {
e3ba567abdf5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content commit 7b6b07d22f3e6fed77b2c237de2b0d96fa939711"
iuc
parents: 1
diff changeset
88 write.table(output[, c(1, 2)], file = length,
e3ba567abdf5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content commit 7b6b07d22f3e6fed77b2c237de2b0d96fa939711"
iuc
parents: 1
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89 col.names = FALSE, row.names = FALSE,
e3ba567abdf5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content commit 7b6b07d22f3e6fed77b2c237de2b0d96fa939711"
iuc
parents: 1
diff changeset
90 quote = FALSE, sep = "\t")
e3ba567abdf5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content commit 7b6b07d22f3e6fed77b2c237de2b0d96fa939711"
iuc
parents: 1
diff changeset
91 }
0
2ca1baabdae0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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92
2ca1baabdae0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
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93
2ca1baabdae0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
iuc
parents:
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94 sessionInfo()