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Fixed a bug for parameter -ref;Updated output message
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@wenbostar
wenbostar committed Sep 25, 2018
1 parent 4c9c5b4 commit 94a765d
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Showing 3 changed files with 161 additions and 62 deletions.
7 changes: 7 additions & 0 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,13 @@

<dependencies>

<!-- https://mvnrepository.com/artifact/commons-cli/commons-cli -->
<dependency>
<groupId>commons-cli</groupId>
<artifactId>commons-cli</artifactId>
<version>1.4</version>
</dependency>


<dependency>
<groupId>org.apache.commons</groupId>
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119 changes: 75 additions & 44 deletions src/main/java/DbCreator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,10 @@
import org.apache.commons.lang3.StringUtils;

import java.io.*;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
import java.util.concurrent.ExecutorService;
Expand Down Expand Up @@ -56,9 +59,9 @@ public class DbCreator {
* @param mRNA_db *_refGeneMrna.fa
* @param gene_anno_file *__refGene.txt
*/
public DbCreator(String mRNA_db, String gene_anno_file){
public DbCreator(String mRNA_db, String gene_anno_file, BufferedWriter logWriter){
try {
this.readAnnotationData(mRNA_db,gene_anno_file);
this.readAnnotationData(mRNA_db,gene_anno_file,logWriter);
} catch (IOException e) {
e.printStackTrace();
}
Expand Down Expand Up @@ -93,7 +96,7 @@ public static void main(String[] args) throws ParseException, IOException {
options.addOption("h", false, "Help");


CommandLineParser parser = new PosixParser();
CommandLineParser parser = new DefaultParser();
CommandLine cmd = parser.parse(options, args);
if (cmd.hasOption("h") || cmd.hasOption("help") || args.length == 0) {
HelpFormatter f = new HelpFormatter();
Expand All @@ -103,20 +106,34 @@ public static void main(String[] args) throws ParseException, IOException {
System.exit(0);
}


String geneAnno = cmd.getOptionValue("r");
String genefa = cmd.getOptionValue("d");

DbCreator createDB4Annovar = new DbCreator(genefa,geneAnno);

String outdir = "./";
if(cmd.hasOption("o")){
createDB4Annovar.outdir = cmd.getOptionValue("o");
File OD = new File(createDB4Annovar.outdir);
outdir = cmd.getOptionValue("o");
File OD = new File(outdir);
if(!OD.isDirectory()){
OD.mkdirs();
}
}

DateFormat dateFormat = new SimpleDateFormat("yyyy/MM/dd HH:mm:ss");
Date date = new Date();

String logfile = outdir+"/log.txt";
System.out.println("log file:"+logfile);

BufferedWriter logWriter = new BufferedWriter(new FileWriter(new File(logfile)));
logWriter.write(dateFormat.format(date)+"\n");
logWriter.write("Command line:"+StringUtils.join(args," ")+"\n");


String geneAnno = cmd.getOptionValue("r");
String genefa = cmd.getOptionValue("d");

DbCreator createDB4Annovar = new DbCreator(genefa,geneAnno,logWriter);

createDB4Annovar.outdir = outdir;


boolean includeRefProteins = false;
if(cmd.hasOption("t")){
includeRefProteins = true;
Expand Down Expand Up @@ -161,7 +178,7 @@ public static void main(String[] args) throws ParseException, IOException {
for (int i = 1; i < d.length; i++) {
System.out.println(" => "+h[i]+" => "+ d[i]);
String prefix = sample_name + "-" + h[i];
ArrayList<String> rfile = createDB4Annovar.run(d[i], prefix, false,true, true);
ArrayList<String> rfile = createDB4Annovar.run(d[i], prefix, false,true, true,logWriter);
// h[i] is sample name
smap.put(h[i], rfile);

Expand All @@ -174,7 +191,7 @@ public static void main(String[] args) throws ParseException, IOException {
// merge
System.out.println("Merge ...");
String oprefix = IFL.getName().replaceAll(".txt","");
createDB4Annovar.merge(resfileMap, hList, oprefix, includeRefProteins);
createDB4Annovar.merge(resfileMap, hList, oprefix, includeRefProteins,logWriter);
}else{

String annovarRes = cmd.getOptionValue("i");
Expand All @@ -185,24 +202,30 @@ public static void main(String[] args) throws ParseException, IOException {
}else{
oprefix = "merge";
}
createDB4Annovar.run(annovarRes,oprefix, includeRefProteins, verbose,true);
if(cmd.hasOption("ref")){
createDB4Annovar.outputRefProteinDB = cmd.getOptionValue("ref");
}else{
createDB4Annovar.outputRefProteinDB = "";
}
createDB4Annovar.run(annovarRes,oprefix, includeRefProteins, verbose,true,logWriter);

if(!createDB4Annovar.outputRefProteinDB.isEmpty()){
createDB4Annovar.addReferenceProteins(createDB4Annovar.gMap, createDB4Annovar.outputRefProteinDB);
}

}

}
if(cmd.hasOption("ref")){
createDB4Annovar.outputRefProteinDB = cmd.getOptionValue("ref");
}else{
createDB4Annovar.outputRefProteinDB = "";
}

if(!createDB4Annovar.outputRefProteinDB.isEmpty()){
System.out.println("Reference protein db:"+createDB4Annovar.outputRefProteinDB);
createDB4Annovar.addReferenceProteins(createDB4Annovar.gMap, createDB4Annovar.outputRefProteinDB,logWriter);
}else{
System.out.println(createDB4Annovar.outputRefProteinDB);
}

logWriter.close();

}

public void merge(HashMap<String,HashMap<String,ArrayList<String>>> resfileMap, ArrayList<String> h, String prefix, boolean addRef) throws IOException {

public void merge(HashMap<String,HashMap<String,ArrayList<String>>> resfileMap, ArrayList<String> h, String prefix, boolean addRef, BufferedWriter logWriter) throws IOException {

HashMap<String, JVariant> mergeVarMap = new HashMap<>();

Expand All @@ -218,9 +241,9 @@ public void merge(HashMap<String,HashMap<String,ArrayList<String>>> resfileMap,
String annofile = resfileMap.get(sample_name).get(fileClass).get(0);
String varfa = resfileMap.get(sample_name).get(fileClass).get(1);

System.out.println("Read " + annofile);
System.out.println("Read " + varfa + "\n");
HashMap<String, JVariant> varMap = readData(annofile, varfa);
logWriter.write("Read " + annofile+"\n");
logWriter.write("Read " + varfa + "\n");
HashMap<String, JVariant> varMap = readData(annofile, varfa,logWriter);

// varID => String varID = d[hMap.get("Chr")]+"_"+d[hMap.get("Start")]+"_"+d[hMap.get("End")]+"_"+d[hMap.get("Ref")]+"_"+d[hMap.get("Alt")]+"_"+d[hMap.get("mRNA")];
String sample_head = sample_name + " " + fileClass;
Expand Down Expand Up @@ -283,7 +306,7 @@ public void merge(HashMap<String,HashMap<String,ArrayList<String>>> resfileMap,
}

if(addRef){
addReferenceProteins(gMap, pWriter);
addReferenceProteins(gMap, pWriter, logWriter);
}

annoWriter.close();
Expand All @@ -296,7 +319,7 @@ public void merge(HashMap<String,HashMap<String,ArrayList<String>>> resfileMap,
}


public HashMap<String, JVariant> readData(String annofile, String varfa) throws IOException {
public HashMap<String, JVariant> readData(String annofile, String varfa, BufferedWriter logWriter) throws IOException {


HashMap<String,String> proMap = new HashMap<>();
Expand Down Expand Up @@ -342,7 +365,7 @@ public HashMap<String, JVariant> readData(String annofile, String varfa) throws
jVariant.protein_seq = proMap.get(d[hMap.get("Variant_ID")]);
jVariant.protein_header = proInfoMap.get(d[hMap.get("Variant_ID")]);
}else{
System.err.println("Don't find protein sequence for variant: "+ d[hMap.get("Variant_ID")] + "("+line+") in file "+annofile+", "+varfa);
logWriter.write("Don't find protein sequence for variant: "+ d[hMap.get("Variant_ID")] + "("+line+") in file "+annofile+", "+varfa+"\n");
continue;
}

Expand All @@ -356,7 +379,7 @@ public HashMap<String, JVariant> readData(String annofile, String varfa) throws
}


private ArrayList<String> run(String variantAnno, String outfilePrefix, boolean addRef, boolean verbose, boolean addAnnoInfo) throws IOException {
private ArrayList<String> run(String variantAnno, String outfilePrefix, boolean addRef, boolean verbose, boolean addAnnoInfo, BufferedWriter logWriter) throws IOException {

////////////////////////////////////////////////////////////////////////////////////////////////////
// output variant information
Expand Down Expand Up @@ -480,6 +503,7 @@ private ArrayList<String> run(String variantAnno, String outfilePrefix, boolean
Matcher m2 = p2.matcher(AAChange_Gene);
if(!m2.find()){
System.err.println("Error: invalid record found in exonic_variant_function file (exonic format error): <"+line+">");
logWriter.write("Error: invalid record found in exonic_variant_function file (exonic format error): <"+line+">"+"\n");
System.exit(1);
}

Expand Down Expand Up @@ -571,7 +595,7 @@ private ArrayList<String> run(String variantAnno, String outfilePrefix, boolean
ref = "REF";
obs = mc9.group(3);
}else{
System.err.println("Warning: invalid coding change format: <"+cchange+">"+ " within <"+ md[i]);
logWriter.write("Warning: invalid coding change format: <"+cchange+">"+ " within <"+ md[i]+"\n");
continue;
}

Expand Down Expand Up @@ -622,6 +646,7 @@ private ArrayList<String> run(String variantAnno, String outfilePrefix, boolean
HashMap<String,Integer> flagged_transcript = new HashMap<>();

System.out.println("Transcripts with variant: "+vMap.size());
logWriter.write("Transcripts with variant: "+vMap.size()+"\n");

int nvar = 0;

Expand All @@ -635,7 +660,7 @@ private ArrayList<String> run(String variantAnno, String outfilePrefix, boolean
for(String vID: vMap.keySet()){
for(JVariant jv : vMap.get(vID)){
nvar++;
fixedThreadPool.execute(new TranslateVariantWorker(jv,nvar,verbose));
fixedThreadPool.execute(new TranslateVariantWorker(jv,nvar,verbose,logWriter));
}
}

Expand All @@ -659,6 +684,7 @@ private ArrayList<String> run(String variantAnno, String outfilePrefix, boolean
pWriter.write(jv.protein_seq + "\n");
}else{
System.err.println("Protein length is zero: "+jv.ID);
logWriter.write("Protein length is zero: "+jv.ID+"\n");
}
}
}
Expand All @@ -669,7 +695,7 @@ private ArrayList<String> run(String variantAnno, String outfilePrefix, boolean

// Add the reference protein sequences into the output database
if(addRef){
addReferenceProteins(gMap,pWriter);
addReferenceProteins(gMap,pWriter,logWriter);
}

pWriter.close();
Expand All @@ -685,7 +711,7 @@ private ArrayList<String> run(String variantAnno, String outfilePrefix, boolean

}

public void readAnnotationData(String db, String geneAnno) throws IOException {
public void readAnnotationData(String db, String geneAnno, BufferedWriter logWriter) throws IOException {
////////////////////////////////////////////////////////////////////////////////////////////////////
// read mRNA DNA sequences: hg19_refGeneMrna.fa
File dbFile = new File(db);
Expand Down Expand Up @@ -732,6 +758,7 @@ public void readAnnotationData(String db, String geneAnno) throws IOException {

}
System.out.println("Read mRNA sequences: "+num);
logWriter.write("Read mRNA sequences: "+num+"\n");
it.close();
dbReader.close();

Expand All @@ -753,6 +780,7 @@ public void readAnnotationData(String db, String geneAnno) throws IOException {
String d[] = line.split("\t");
if(d.length<11){
System.err.println("Error: invalid record found in gene file (>=11 fields expected): <"+line+">");
logWriter.write("Error: invalid record found in gene file (>=11 fields expected): <"+line+">"+"\n");
System.exit(1);
}

Expand Down Expand Up @@ -800,14 +828,14 @@ public void readAnnotationData(String db, String geneAnno) throws IOException {
}

if(!gMap.containsKey(name)){
System.out.println("Warning: remove ("+name+") "+line);
logWriter.write("Warning: remove ("+name+") "+line+"\n");
continue;
}

if(!gMap.get(name).infor.isEmpty()){
String infor = chr+":"+exonstart.split(",")[0];
if(!gMap.get(name).infor.equalsIgnoreCase(infor)){
System.out.println("Warning: remove (used "+name+" "+gMap.get(name).infor+") "+line);
logWriter.write("Warning: remove (used "+name+" "+gMap.get(name).infor+") "+line+"\n");
continue;
}
}
Expand Down Expand Up @@ -899,10 +927,11 @@ public void readAnnotationData(String db, String geneAnno) throws IOException {
}
}
System.out.println("Remove transcripts: "+n_remove_transcript);
logWriter.write("Remove transcripts: "+n_remove_transcript+"\n");

}

public void addReferenceProteins(HashMap<String,JTranscript> gMap, BufferedWriter pWriter){
public void addReferenceProteins(HashMap<String,JTranscript> gMap, BufferedWriter pWriter, BufferedWriter logWriter) throws IOException {

Pattern pStop = Pattern.compile("\\*.+");
int nrefProteins = 0;
Expand All @@ -921,13 +950,13 @@ public void addReferenceProteins(HashMap<String,JTranscript> gMap, BufferedWrite
dna_seq = gMap.get(transcript).mRNA_seq.substring(gMap.get(transcript).start-1, gMap.get(transcript).end);
} catch (StringIndexOutOfBoundsException e) {
e.printStackTrace();
System.out.println(transcript+"\t"+gMap.get(transcript).mRNA_seq.length()+"\t"+gMap.get(transcript).start+"\t"+gMap.get(transcript).end);
logWriter.write(transcript+"\t"+gMap.get(transcript).mRNA_seq.length()+"\t"+gMap.get(transcript).start+"\t"+gMap.get(transcript).end+"\n");
System.exit(1);
}
String protein = translateDNA(dna_seq);
String protein = translateDNA(dna_seq,logWriter);
Matcher pStopMatcher = pStop.matcher(protein);
if(pStopMatcher.find()){
System.out.println("Warning:"+transcript+" "+gMap.get(transcript).cds_start+" "+ gMap.get(transcript).cds_end+"\t"+protein);
logWriter.write("Warning:"+transcript+" "+gMap.get(transcript).cds_start+" "+ gMap.get(transcript).cds_end+"\t"+protein+"\n");
}

protein = protein.replaceAll("\\*.*$","");
Expand All @@ -943,17 +972,18 @@ public void addReferenceProteins(HashMap<String,JTranscript> gMap, BufferedWrite

}
System.out.println("Reference proteins: "+nrefProteins);
logWriter.write("Reference proteins: "+nrefProteins+"\n");

}

public void addReferenceProteins(HashMap<String,JTranscript> gMap, String file) throws IOException {
public void addReferenceProteins(HashMap<String,JTranscript> gMap, String file, BufferedWriter logWriter) throws IOException {
BufferedWriter pWriter = new BufferedWriter(new FileWriter(new File(file)));
addReferenceProteins(gMap,pWriter);
addReferenceProteins(gMap,pWriter,logWriter);
pWriter.close();
}


public static String translateDNA(String dna){
public static String translateDNA(String dna,BufferedWriter logWriter) throws IOException {
String protein = "";
dna = dna.toUpperCase();
Pattern p3 = Pattern.compile("(...)");
Expand All @@ -964,6 +994,7 @@ public static String translateDNA(String dna){
protein = protein+codons.get(t3);
}else{
System.err.println("Error: invalid triplets found in DNA sequence to be translated: <"+t3+"> in <"+dna+">");
logWriter.write("Error: invalid triplets found in DNA sequence to be translated: <"+t3+"> in <"+dna+">"+"\n");
System.exit(1);
}
}
Expand Down
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