Mercurial > repos > proteore > proteore_kegg_pathways_coverage
changeset 0:8883a7173cba draft
planemo upload commit 63302cb49d4f0f4dbc9ae141d20704822588f54e-dirty
| author | proteore |
|---|---|
| date | Mon, 12 Nov 2018 10:59:49 -0500 |
| parents | |
| children | 7004924a3686 |
| files | compute_kegg_pathways.R compute_kegg_pathways.xml test-data/SPZ.soluble.txt |
| diffstat | 3 files changed, 3670 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/compute_kegg_pathways.R Mon Nov 12 10:59:49 2018 -0500 @@ -0,0 +1,152 @@ +options(warn=-1) #TURN OFF WARNINGS !!!!!! + +suppressMessages(library(KEGGREST)) + +get_args <- function(){ + + ## Collect arguments + args <- commandArgs(TRUE) + + ## Default setting when no arguments passed + if(length(args) < 1) { + args <- c("--help") + } + + ## Help section + if("--help" %in% args) { + cat("Pathview R script + Arguments: + --help Print this test + --input tab file + --id_list id list ',' separated + --id_type type of input ids (kegg-id, uniprot_AC,geneID) + --id_column number og column containg ids of interest + --nb_pathways number of pathways to return + --header boolean + --output output path + --species species used to get specific pathways (hsa,mmu,rno) + + Example: + Rscript keggrest.R --input='P31946,P62258' --id_type='uniprot' --id_column 'c1' --header TRUE \n\n") + + q(save="no") + } + + parseArgs <- function(x) strsplit(sub("^--", "", x), "=") + argsDF <- as.data.frame(do.call("rbind", parseArgs(args))) + args <- as.list(as.character(argsDF$V2)) + names(args) <- argsDF$V1 + + return(args) +} + +str2bool <- function(x){ + if (any(is.element(c("t","true"),tolower(x)))){ + return (TRUE) + }else if (any(is.element(c("f","false"),tolower(x)))){ + return (FALSE) + }else{ + return(NULL) + } +} + +read_file <- function(path,header){ + file <- try(read.csv(path,header=header, sep="\t",stringsAsFactors = FALSE, quote="\"", check.names = F),silent=TRUE) + if (inherits(file,"try-error")){ + stop("File not found !") + }else{ + return(file) + } +} + +get_pathways_list <- function(species){ + ##all available pathways for the species + pathways <-keggLink("pathway", species) + tot_path<-unique(pathways) + + ##formating the dat into a list object + ##key= pathway ID, value = genes of the pathway in the kegg format + pathways_list <- sapply(tot_path, function(pathway) names(which(pathways==pathway))) + return (pathways_list) +} + +get_list_from_cp <-function(list){ + list = strsplit(list, "[ \t\n]+")[[1]] + list = list[list != ""] #remove empty entry + list = gsub("-.+", "", list) #Remove isoform accession number (e.g. "-2") + return(list) +} + +geneID_to_kegg <- function(vector,species){ + vector <- sapply(vector, function(x) paste(species,x,sep=":"),USE.NAMES = F) + return (vector) +} + +kegg_mapping<- function(kegg_id_list,id_type,ref_ids) { + + #convert to KEGG ID + #if (id_type!="kegg-id"){ + # id_list <- unique(sapply(id_list, function(x) paste(id_type,":",x,sep=""),USE.NAMES = F)) + # if (length(id_list)>250){ + # id_list <- split(id_list, ceiling(seq_along(id_list)/250)) + # id_list <- sapply(id_list, function(x) keggConv("genes",x)) + # kegg_id_list <- unique(unlist(id_list)) + # } else { + # kegg_id_list <- unique(keggConv("genes", id_list)) + # } + #} else { + # kegg_id_list <- unique(id_list) + #} + + #mapping + map<-lapply(ref_ids, is.element, unique(kegg_id_list)) + names(map) <- sapply(names(map), function(x) gsub("path:","",x),USE.NAMES = FALSE) #remove the prefix "path:" + + in.path<-sapply(map, function(x) length(which(x==TRUE))) + tot.path<-sapply(map, length) + + ratio <- (as.numeric(in.path[which(in.path!=0)])) / (as.numeric(tot.path[which(in.path!=0)])) + ratio <- as.numeric(format(round(ratio*100, 2), nsmall = 2)) + + ##useful but LONG + ## to do before : in step 1 + path.names<-names(in.path[which(in.path!=0)]) + name <- sapply(path.names, function(x) keggGet(x)[[1]]$NAME,USE.NAMES = FALSE) + + res<-data.frame(I(names(in.path[which(in.path!=0)])), I(name), ratio, as.numeric(in.path[which(in.path!=0)]), as.numeric(tot.path[which(in.path!=0)])) + res <- res[order(as.numeric(res[,3]),decreasing = TRUE),] + colnames(res)<-c("pathway_ID", "Description" , "Ratio IDs mapped/total IDs (%)" ,"nb KEGG genes IDs mapped in the pathway", "nb total of KEGG genes IDs present in the pathway") + + return(res) + +} + +#get args from command line +args <- get_args() + +#save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/kegg_pathways_identification/args.Rda") +#load("/home/dchristiany/proteore_project/ProteoRE/tools/kegg_pathways_identification/args.Rda") + +###setting variables +header = str2bool(args$header) +if (!is.null(args$id_list)) {id_list <- get_list_from_cp(args$id_list)} +if (!is.null(args$input)) { + csv <- read_file(args$input,header) + ncol <- as.numeric(gsub("c", "" ,args$id_column)) + id_list <- as.vector(csv[,ncol]) + id_list <- id_list[which(!is.na(id_list))] +} +if (args$id_type == "ncbi-geneid") { + id_list <- geneID_to_kegg(id_list,args$species) +} + + +#get pathways of species with associated KEGG ID genes +pathways_list <- get_pathways_list(args$species) + +#mapping on pathways +res <- kegg_mapping(id_list,args$id_type,pathways_list) +if (nrow(res) > as.numeric(args$nb_pathways)) { res <- res[1:args$nb_pathways,] } + +write.table(res, file=args$output, quote=FALSE, sep='\t',row.names = FALSE, col.names = TRUE) +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/compute_kegg_pathways.xml Mon Nov 12 10:59:49 2018 -0500 @@ -0,0 +1,138 @@ +<tool id="compute_kegg_pathways" name="KEGG pathways" version="2018.11.12"> + <description>identification and coverage</description> + <requirements> + <requirement type="package" version="1.18.0">bioconductor-keggrest</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + Rscript $__tool_directory__/compute_kegg_pathways.R + + #if $input.ids == "text" + --id_list="$input.txt" + #else + --input="$input.file" + --id_column="$input.ncol" + --header="$input.header" + #end if + + --id_type="$id_type" + --output="$output1" + --nb_pathways="$nb_pathways" + --species="$species" + + ]]></command> + <inputs> + <conditional name="input" > + <param name="ids" type="select" label="Enter your identifiers (KEGG genes ID)" help="Copy/paste or ID list from a file (e.g. table)" > + <option value="text">Copy/paste your identifiers</option> + <option value="file" selected="true">Input file containing your KEGG genes IDs</option> + </param> + <when value="text" > + <param name="txt" type="text" label="Copy/paste your identifiers" help='IDs must be separated by tab,space or carriage return into the form field, for example: hsa:3306 hsa:22948' > + <sanitizer invalid_char=''> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"> + <add source="'" target="__sq__"/> + </mapping> + </sanitizer> + </param> + </when> + <when value="file" > + <param name="file" type="data" format="txt,tabular,tsv" label="Select a file that contains your list of KEGG gene IDs" help="" /> + <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" /> + <param name="ncol" type="text" value="c1" label="The column number of KEGG genes IDs to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' /> + </when> + </conditional> + <param name="id_type" type="select" label="select your identifiers type :"> + <option value="kegg-id">KEGG ID (genes)</option> + <!--option value="uniprot">Uniprot Accession number</option--> + <option value="ncbi-geneid">Entrez gene ID</option> + </param> + <param name="species" type="select" label="Select species"> + <option value="hsa">Human (H. sapiens)</option> + <option value="mmu">Mouse (M. musculus)</option> + <option value="rno">Rat (R. norvegicus)</option> + </param> + <param type="integer" name="nb_pathways" label="Set the number of pathways to be displayed in the output" value="10" help="Pathways are sorted by percent of mapping gene by pathway in descending order"/> + </inputs> + <outputs> + <data name="output1" format="tsv" /> + </outputs> + <tests> + <test> + <conditional name="input" > + <param name="ids" value="file"/> + <param name="file" value="SPZ.soluble_kegg_id.txt" /> + <param name="header" value="true" /> + <param name="ncol" value="c2" /> + </conditional> + <param name="id_type" value="kegg-id" /> + <param name="species" value="hsa" /> + <param name="nb_pathways" value="20" /> + <output name="output1" value="test.tsv" /> + </test> + </tests> + <help><![CDATA[ + +This tool maps a list of KEGG gene IDs to KEGG pathway and return a list of KEGG pathways ranked by the percentage of coverage for each pathway; this is done by computing the number of KEGG genes IDs from your list divided by the total number of KEGG genes present in the considered species for each KEGG pathway. + +It allows you to directly identify the signaling pathways that are the most covered by your proteomics dataset. + +By default the number of pathway to be displayed is set to 10 and sorted in descending order. + +At the moment three species are supported: Human (Homo sapiens), Mouse (Mus musculus) and Rat (Rattus norvegicus). + +**Input:** + +Input can be either a list of KEGG genes IDs or a file containing multiple columns but with at least one column of KEGG genes IDs (e.g. hsa04970). If your input file contains other type of IDs, please use the ID_Converter tool to get KEGG genes ID. + +**Output:** + +The output is a tabular file (.tsv) with the following columns: + +* **Pathway_ID:** KEGG pathway identifier (e.g. hsa04970) +* **Description:** name of the pathway as in KEGG +* **Ratio IDs mapped/total IDs (%):** percentage of pathway coverage +* **nb KEGG genes IDs mapped in the pathway:** number of KEGG genes of your list mapped on the KEGG pathway +* **nb total of KEGG genes IDs present in the pathway:** total number of KEGG genes present in the KEGG pathway + +----- + +.. class:: infomark + +**Database:** + +Pathways and KEGG genes IDs are collected via KEGGREST package. + +User manual / Documentation: KEGGREST Bioconductor package https://bioconductor.org/packages/3.1/bioc/html/KEGGREST.html + + +----- + +.. class:: infomark + +**Galaxy integration** + +David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR + +Sandra Dérozier, Olivier Rué, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform + +This work has been partially funded through the French National Agency for Research (ANR) IFB project. + +Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. + + ]]></help> + <citations> + <citation type="bibtex"> +@misc{githubKEGGREST, + title = {KEGGREST: Client-side REST access to KEGG}, + author = {Dan Tenenbaum}, + year = {2018}, + note = {R package version 1.18.1}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/Bioconductor/KEGGREST}, +}</citation> + </citations> +</tool>
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