Mercurial > repos > proteore > proteore_kegg_pathways_coverage

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/compute_kegg_pathways.R	Wed Sep 19 05:38:52 2018 -0400
@@ -0,0 +1,112 @@
+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 (uniprot_AC or geneID)
+      --id_column             number og column containg ids of interest
+      --nb_pathways           number of pathways to return
+      --header                boolean
+      --output                output path
+      --ref                  ref file (l.hsa.gene.RData, l.hsa.up.RData, l.mmu.up.Rdata)
+
+      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)
+}
+
+args <- get_args()
+
+#save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/compute_KEGG_pathways/args.Rda")
+#load("/home/dchristiany/proteore_project/ProteoRE/tools/compute_KEGG_pathways/args.Rda")
+
+##function arguments :
+## id.ToMap = input from the user to map on the pathways = list of IDs
+## idType : must be "UNIPROT" or "ENTREZ"
+## org : for the moment can be "Hs" only. Has to evoluate to "Mm"
+
+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.table(path,header=header, sep="\t",stringsAsFactors = FALSE, quote=""),silent=TRUE)
+  if (inherits(file,"try-error")){
+    stop("File not found !")
+  }else{
+    return(file)
+  }
+}
+
+ID2KEGG.Mapping<- function(id.ToMap,ref) {
+
+    ref_ids = get(load(ref))
+    map<-lapply(ref_ids, is.element, unique(id.ToMap))
+    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]]$NAME,USE.NAMES = FALSE)
+
+    res<-data.frame(I(names(in.path[which(in.path!=0)])), I(name), ratio, as.numeric(in.path[which(in.path!=0)]), as.numeric(tot.path[which(in.path!=0)]))
+    res <- res[order(as.numeric(res[,3]),decreasing = TRUE),]
+    colnames(res)<-c("pathway_ID", "Description" , "Ratio IDs mapped/total IDs (%)" ,"nb genes mapped in the pathway", "nb total genes present in the pathway")
+
+    return(res)
+
+}
+
+###setting variables
+header = str2bool(args$header)
+if (!is.null(args$id_list)) {id_list <- strsplit(args$id_list,",")[[1]]}
+if (!is.null(args$input)) {
+  csv <- read_file(args$input,header)
+  ncol <- as.numeric(gsub("c", "" ,args$id_column))
+  id_list <- as.vector(csv[,ncol])
+}
+id_type <- toupper(args$id_type)
+
+#mapping on pathways
+res <- ID2KEGG.Mapping(id_list,args$ref)
+if (nrow(res) > as.numeric(args$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	Wed Sep 19 05:38:52 2018 -0400
@@ -0,0 +1,153 @@
+<tool id="compute_kegg_pathways" name="KEGG pathways coverage" version="2018.09.18">
+    <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="$input.header"
+        #end if
+
+        --id_type="$ref_ids.id_type"
+        --output="$output1"
+        --nb_pathways="$nb_pathways"
+        --ref="$__tool_directory__/$ref_ids.ref_file"
+
+    ]]></command>
+    <inputs>
+        <conditional name="input" >
+            <param name="ids" type="select" label="Provide your identifiers (Uniprot or Entrez gene)" 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 identifiers</option>
+            </param>
+            <when value="text" >
+                <param name="txt" type="text" label="Copy/paste your identifiers" help='IDs must be separated by "," into the form field, for example: P31946,P62258' >
+                    <sanitizer invalid_char=''>
+                        <valid initial="string.printable">
+                            <remove value="&apos;"/>
+                        </valid>
+                        <mapping initial="none">
+                            <add source="&apos;" target="__sq__"/>
+                        </mapping>
+                    </sanitizer>
+                </param>
+            </when>
+            <when value="file" >
+                <param name="file" type="data" format="txt,tabular" label="Select a file that contains your list of 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 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>
+        <conditional name="ref_ids">
+            <param name="id_type" type="select" label="select your identifiers type :">
+                <option value="uniprot">Uniprot Accession number</option>
+                <option value="geneID">Entrez gene ID</option>
+            </param>
+            <when value="uniprot">
+                <param name="ref_file" type="select" label="Select species" >
+                    <options from_data_table="uniprot_kegg_list"/>
+                        <option>Human (Homo sapiens)</option>
+                        <option>Mouse (Mus musculus)</option>
+                </param>
+            </when>
+            <when value="geneID">
+                <param name="ref_file" type="select" label="Select species" >
+                    <options from_data_table="entrez_kegg_list"/>
+                        <option>Human (Homo sapiens)</option>
+                        <option>Mouse (Mus musculus)</option>
+                </param>
+            </when>
+        </conditional>
+        <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>
+    <help><![CDATA[
+
+This tool computes the number of proteins from your list divided by the total number of protein of each KEGG pathway.
+
+it allows you to 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 two species are supported: Human (Homo sapiens) and Mouse (Mus musculus)
+
+**Input:**
+
+Input can be either a list of Uniprot accession number or Entrez gene IDs (copy/paste mode) or a file containing multiple columns but with at least one column Uniprot accession number or Entrez gene IDs. If your input file contains other type of IDs, please use the ID_Converter tool.
+
+**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 genes mapped in the pathway:** number of genes/proteins of your list mapped on the KEGG pathway
+* **nb total genes present in the pathway:** total number of genes/proteins present in the KEGG pathway
+
+-----
+
+.. class:: infomark
+
+**Database:**
+
+Pathways and associated Uniprot Accession Number or Gene IDs are collected from 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.
+
+-----
+
+compute_KEGG_pathways R script
+
+| Arguments:
+| --**help**                  Print this test
+| --**input**                 tab file
+| --**id_list**               id list ',' separated
+| --**id_type**               type of input ids (uniprot_AC or geneID)
+| --**id_column**             number og column containg ids of interest
+| --**org**                   organism : Hs , Mm, ...
+| --**nb_pathways**           number of pathways to return
+| --**header**                boolean
+| --**output**                output path
+| --**ref**                   ref file (l.hsa.gene.RData, l.hsa.up.RData)
+|
+| Example:
+| Rscript compute_KEGG_pathways.R --input='P31946,P62258' --id_type='uniprot' --id_column 'c1' --header TRUE
+|
+
+    ]]></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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/entrez_kegg_list.loc.sample	Wed Sep 19 05:38:52 2018 -0400
@@ -0,0 +1,3 @@
+#name	date	organism	value(path)
+Human (Homo sapiens)	27-07-18	hsa	tool-data/l.hsa.gene.RData
+Mouse (Mus musculus)	27-07-18	mmu	tool-data/l.mmu.gene.RData
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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Binary file tool-data/l.hsa.gene.RData has changed
Binary file tool-data/l.hsa.up.RData has changed
Binary file tool-data/l.mmu.gene.RData has changed
Binary file tool-data/l.mmu.up.RData has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Wed Sep 19 05:38:52 2018 -0400
@@ -0,0 +1,12 @@
+<tables>
+    <!-- location uniprot_kegg_list for find pathways tool-->
+    <table name='uniprot_kegg_list' comment_char="#">
+        <columns>name,date,organism,value</columns>
+        <file path="tool-data/uniprot_kegg_list.loc"/>
+    </table>
+    <!-- location entrez_kegg_list for find pathways tool-->
+    <table name='entrez_kegg_list' comment_char="#">
+        <columns>name,date,organism,value</columns>
+        <file path="tool-data/entrez_kegg_list.loc"/>
+    </table>
+</tables>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/uniprot_kegg_list.loc.sample	Wed Sep 19 05:38:52 2018 -0400
@@ -0,0 +1,3 @@
+#name	date	organism	value(path)
+Human (Homo sapiens)	27-07-18	hsa	tool-data/l.hsa.up.RData
+Mouse (Mus musculus)	27-07-18	mmu	tool-data/l.mmu.up.RData