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Modifications to several apps for searching the PMR, running TNRunner,
and parsing vst and tpm values for cBioPortal
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Sep 11, 2023
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,167 @@ | ||
| package edu.expr; | ||
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| import java.io.*; | ||
| import java.util.regex.*; | ||
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| import edu.utah.hci.misc.Gzipper; | ||
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| import java.util.*; | ||
| import util.gen.IO; | ||
| import util.gen.Misc; | ||
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| public class NormalizedCountCBioFormater { | ||
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| private File ensSymIdFile; | ||
| private HashMap<String,String> ensSymIds; | ||
| private File normCountFile; | ||
| private String dupKeyValDelim = ":"; | ||
| private Pattern dupDelim = Pattern.compile(dupKeyValDelim); | ||
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| public NormalizedCountCBioFormater (String[] args){ | ||
| processArgs(args); | ||
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| //load key value file skipping duplicate keys and making duplicate values unique | ||
| IO.pl("Loading Ensembl 2 gene symbol lookup table..."); | ||
| ensSymIds = IO.loadFileIntoHashMapUniqueValues(ensSymIdFile, dupKeyValDelim); | ||
| IO.pl("Number unique ensembl gene IDs "+ensSymIds.size()); | ||
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| //walk the norm count file | ||
| IO.pl("\nParsing "+normCountFile.getName()); | ||
| parseAndSaveMatches(); | ||
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| IO.pl("\nDone!\n"); | ||
| } | ||
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| //here, test and run it! | ||
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| public void parseAndSaveMatches(){ | ||
| try { | ||
| HashSet<String> geneSymbols = new HashSet<String>(); | ||
| File results = new File (normCountFile.getParentFile(), Misc.removeExtension(normCountFile.getName())+"_ForCBio.txt.gz"); | ||
| Gzipper out = new Gzipper (results); | ||
| BufferedReader in = IO.fetchBufferedReader(normCountFile); | ||
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| //read in the header, this is just a dump of the column names | ||
| String line = in.readLine(); | ||
| String[] tokens = Misc.TAB.split(line); | ||
| int numSamples = tokens.length; | ||
| IO.pl("\t"+numSamples+"\t#Samples"); | ||
| out.println("Hugo_Symbol\t"+line); | ||
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| //counters | ||
| int totalLines = 0; | ||
| int numMatches = 0; | ||
| int numNoMatches = 0; | ||
| int numBadColumns = 0; | ||
| int numDuplicateSymbolsSkipped = 0; | ||
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| while ((line = in.readLine())!=null){ | ||
| totalLines++; | ||
| tokens = Misc.TAB.split(line); | ||
| if (tokens.length-1 != numSamples) { | ||
| numBadColumns++; | ||
| IO.el("\tSkipping, incorrect # columns -> "+line); | ||
| continue; | ||
| } | ||
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| //look for the ensembl id in the lookup hash | ||
| String ensId = tokens[0]; | ||
| String geneSymbol = ensSymIds.get(ensId); | ||
| if (geneSymbol!= null) { | ||
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| //does it contain a value delimiter? If so check it | ||
| if (geneSymbol.contains(dupKeyValDelim)) { | ||
| String[] symbolKey = dupDelim.split(geneSymbol); | ||
| //already seen? | ||
| if (geneSymbols.contains(symbolKey[0])) { | ||
| IO.el("\tSkipping, duplicate symbol -> "+geneSymbol+ " line # "+totalLines); | ||
| numDuplicateSymbolsSkipped++; | ||
| continue; | ||
| } | ||
| else { | ||
| geneSymbols.add(symbolKey[0]); | ||
| geneSymbol = symbolKey[0]; | ||
| } | ||
| } | ||
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| //save the line | ||
| numMatches++; | ||
| out.print(geneSymbol); | ||
| for (int i=1; i< tokens.length; i++) { | ||
| out.print("\t"); | ||
| out.print(tokens[i]); | ||
| } | ||
| out.println(); | ||
| } | ||
| else numNoMatches++; | ||
| } | ||
| IO.pl("\t"+totalLines+"\t# Data lines"); | ||
| IO.pl("\t"+numMatches+"\t# Matches written to file"); | ||
| IO.pl("\t"+ numNoMatches+"\t# No Matches"); | ||
| IO.pl("\t"+ numBadColumns+"\t# Incorrect sample number column lines"); | ||
| IO.pl("\t"+ numDuplicateSymbolsSkipped+"\t# Duplicate symbols"); | ||
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| //close the reader and writer IO | ||
| in.close(); | ||
| out.close(); | ||
| } catch (Exception e){ | ||
| e.printStackTrace(); | ||
| } | ||
| } | ||
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| /**This method will process each argument and assign new varibles*/ | ||
| public void processArgs(String[] args){ | ||
| IO.pl("\n"+IO.fetchUSeqVersion()+" Arguments: "+ Misc.stringArrayToString(args, " ") +"\n"); | ||
| Pattern pat = Pattern.compile("-[a-z]"); | ||
| for (int i = 0; i<args.length; i++){ | ||
| String lcArg = args[i].toLowerCase(); | ||
| Matcher mat = pat.matcher(lcArg); | ||
| if (mat.matches()){ | ||
| char test = args[i].charAt(1); | ||
| try{ | ||
| switch (test){ | ||
| case 'n': normCountFile = new File(args[i+1]); i++; break; | ||
| case 'e': ensSymIdFile = new File(args[i+1]); i++; break; | ||
| case 'h': printDocs(); System.exit(0); | ||
| default: Misc.printExit("\nError: unknown option! " + mat.group()); | ||
| } | ||
| } | ||
| catch (Exception e){ | ||
| Misc.printExit("\nSorry, something doesn't look right with this parameter: -"+test+"\n"); | ||
| e.printStackTrace(); | ||
| } | ||
| } | ||
| } | ||
| //check agilentFiles | ||
| if (ensSymIdFile == null ) Misc.printExit("\nCannot find your tab delimited ensembl geneSymbol ID lookup file?\n"); | ||
| if (normCountFile == null) Misc.printExit("\nCannot find your DESeq2 normalized count file?\n"); | ||
| } | ||
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| public static void printDocs(){ | ||
| IO.pl("\n" + | ||
| "**************************************************************************************\n" + | ||
| "** NormalizedCountCBioFormater: August 2023 **\n" + | ||
| "**************************************************************************************\n" + | ||
| "Parses a DESeq2 output file containing normalized counts, converts the ensembl gene\n" + | ||
| "names to HUGO gene symbols, and saves the output ready for import into cBioPortal.\n"+ | ||
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| "-e Path a tab delimited txt file containing Ensembl IDs and Gene Symbols.\n" + | ||
| "-n Path to a normalized count file from DESeq2, e.g. \n"+ | ||
| "write.table(assay(vst(dds, blind=FALSE)), file = 'vst.txt', quote=FALSE, sep ='\\t')'.\n" + | ||
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| "Example: java -jar pathTo/Apps/NormalizedCountCBioFormater -e ensembIDsGeneSym.txt\n"+ | ||
| " -n vst.txt\n" + | ||
| "**************************************************************************************\n"); | ||
| } | ||
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| public static void main(String[] args) { | ||
| if (args.length == 0) { | ||
| printDocs(); | ||
| System.exit(0); | ||
| } | ||
| else new NormalizedCountCBioFormater(args); | ||
| } | ||
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| } |
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