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make temp matrix file when calling poa
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@hsnguyen
hsnguyen committed Oct 18, 2019
1 parent f3382bf commit c8ff335
Showing 1 changed file with 82 additions and 15 deletions.
97 changes: 82 additions & 15 deletions src/main/java/japsa/bio/np/ErrorCorrection.java
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Original file line number Diff line number Diff line change
Expand Up @@ -34,8 +34,12 @@
package japsa.bio.np;

import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.io.PrintWriter;
import java.nio.file.Files;
import java.nio.file.Paths;
import java.util.ArrayList;
Expand Down Expand Up @@ -119,34 +123,81 @@ public static void writeAlignmentToFaiFile(List<Sequence> readList,String faiFil

public static void runMultipleAlignment(String faiFile, String faoFile) throws IOException, InterruptedException{
{
String cmd = "";
String[] cmd;
File temp = File.createTempFile("tempfile", ".tmp");
if (msa.startsWith("poa")){
cmd = "poa -read_fasta " + faiFile + " -clustal " + faoFile + " -hb blosum80.mat";
//create a temporary matrix file similar to blosum80.mat
PrintWriter printer = new PrintWriter(new BufferedWriter(new FileWriter(temp)));
printer.println("GAP-PENALTIES=12 6 6");
printer.println(" A R N D C Q E G H I L K M F P S T W Y V B Z X ? a g t c u ] n");
printer.println("A 7 -3 -3 -3 -1 -2 -2 0 -3 -3 -3 -1 -2 -4 -1 2 0 -5 -4 -1 -3 -2 -1 -9 -9 -9 -9 -9 -9 -9 -9\n"
+ "R -3 9 -1 -3 -6 1 -1 -4 0 -5 -4 3 -3 -5 -3 -2 -2 -5 -4 -4 -2 0 -2 -9 -9 -9 -9 -9 -9 -9 -9\n"
+ "N -3 -1 9 2 -5 0 -1 -1 1 -6 -6 0 -4 -6 -4 1 0 -7 -4 -5 5 -1 -2 -9 -9 -9 -9 -9 -9 -9 -9\n"
+ "D -3 -3 2 10 -7 -1 2 -3 -2 -7 -7 -2 -6 -6 -3 -1 -2 -8 -6 -6 6 1 -3 -9 -9 -9 -9 -9 -9 -9 -9\n"
+ "C -1 -6 -5 -7 13 -5 -7 -6 -7 -2 -3 -6 -3 -4 -6 -2 -2 -5 -5 -2 -6 -7 -4 -9 -9 -9 -9 -9 -9 -9 -9\n"
+ "Q -2 1 0 -1 -5 9 3 -4 1 -5 -4 2 -1 -5 -3 -1 -1 -4 -3 -4 -1 5 -2 -9 -9 -9 -9 -9 -9 -9 -9\n"
+ "E -2 -1 -1 2 -7 3 8 -4 0 -6 -6 1 -4 -6 -2 -1 -2 -6 -5 -4 1 6 -2 -9 -9 -9 -9 -9 -9 -9 -9\n"
+ "G 0 -4 -1 -3 -6 -4 -4 9 -4 -7 -7 -3 -5 -6 -5 -1 -3 -6 -6 -6 -2 -4 -3 -9 -9 -9 -9 -9 -9 -9 -9\n"
+ "H -3 0 1 -2 -7 1 0 -4 12 -6 -5 -1 -4 -2 -4 -2 -3 -4 3 -5 -1 0 -2 -9 -9 -9 -9 -9 -9 -9 -9\n"
+ "I -3 -5 -6 -7 -2 -5 -6 -7 -6 7 2 -5 2 -1 -5 -4 -2 -5 -3 4 -6 -6 -2 -9 -9 -9 -9 -9 -9 -9 -9\n"
+ "L -3 -4 -6 -7 -3 -4 -6 -7 -5 2 6 -4 3 0 -5 -4 -3 -4 -2 1 -7 -5 -2 -9 -9 -9 -9 -9 -9 -9 -9\n"
+ "K -1 3 0 -2 -6 2 1 -3 -1 -5 -4 8 -3 -5 -2 -1 -1 -6 -4 -4 -1 1 -2 -9 -9 -9 -9 -9 -9 -9 -9\n"
+ "M -2 -3 -4 -6 -3 -1 -4 -5 -4 2 3 -3 9 0 -4 -3 -1 -3 -3 1 -5 -3 -2 -9 -9 -9 -9 -9 -9 -9 -9\n"
+ "F -4 -5 -6 -6 -4 -5 -6 -6 -2 -1 0 -5 0 10 -6 -4 -4 0 4 -2 -6 -6 -3 -9 -9 -9 -9 -9 -9 -9 -9\n"
+ "P -1 -3 -4 -3 -6 -3 -2 -5 -4 -5 -5 -2 -4 -6 12 -2 -3 -7 -6 -4 -4 -2 -3 -9 -9 -9 -9 -9 -9 -9 -9\n"
+ "S 2 -2 1 -1 -2 -1 -1 -1 -2 -4 -4 -1 -3 -4 -2 7 2 -6 -3 -3 0 -1 -1 -9 -9 -9 -9 -9 -9 -9 -9\n"
+ "T 0 -2 0 -2 -2 -1 -2 -3 -3 -2 -3 -1 -1 -4 -3 2 8 -5 -3 0 -1 -2 -1 -9 -9 -9 -9 -9 -9 -9 -9\n"
+ "W -5 -5 -7 -8 -5 -4 -6 -6 -4 -5 -4 -6 -3 0 -7 -6 -5 16 3 -5 -8 -5 -5 -9 -9 -9 -9 -9 -9 -9 -9\n"
+ "Y -4 -4 -4 -6 -5 -3 -5 -6 3 -3 -2 -4 -3 4 -6 -3 -3 3 11 -3 -5 -4 -3 -9 -9 -9 -9 -9 -9 -9 -9\n"
+ "V -1 -4 -5 -6 -2 -4 -4 -6 -5 4 1 -4 1 -2 -4 -3 0 -5 -3 7 -6 -4 -2 -9 -9 -9 -9 -9 -9 -9 -9\n"
+ "B -3 -2 5 6 -6 -1 1 -2 -1 -6 -7 -1 -5 -6 -4 0 -1 -8 -5 -6 6 0 -3 -9 -9 -9 -9 -9 -9 -9 -9\n"
+ "Z -2 0 -1 1 -7 5 6 -4 0 -6 -5 1 -3 -6 -2 -1 -2 -5 -4 -4 0 6 -1 -9 -9 -9 -9 -9 -9 -9 -9\n"
+ "X -1 -2 -2 -3 -4 -2 -2 -3 -2 -2 -2 -2 -2 -3 -3 -1 -1 -5 -3 -2 -3 -1 -2 -9 -9 -9 -9 -9 -9 -9 -9\n"
+ "? -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9\n"
+ "a -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 4 -2 -2 -2 -2 -9 0\n"
+ "g -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -2 4 -2 -2 -2 -9 0\n"
+ "t -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -2 -2 4 -2 4 -9 0\n"
+ "c -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -2 -2 -2 4 -2 -9 0\n"
+ "u -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -2 -2 4 -2 4 -9 0\n"
+ "] -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9\n"
+ "n -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 -9 0 0 0 0 0 -9 0");

printer.close();
//invoke
cmd = new String[]{"poa", "-read_fasta", faiFile, "-clustal", faoFile, "-hb", temp.getAbsolutePath()};

}else if (msa.startsWith("spoa")){
cmd = new String[]{"spoa", faiFile};
}else if (msa.startsWith("muscle")){
cmd = "muscle -in " + faiFile + " -out " + faoFile + " -maxiters 5 -quiet";
cmd = new String[]{"muscle", "-in", faiFile, "-out", faoFile, "-maxiters", "5", "-quiet"};
}else if (msa.startsWith("clustal")) {
cmd = "clustalo --force -i " + faiFile + " -o " + faoFile;
cmd = new String[]{"clustalo", "--force", "-i", faiFile, "-o", faoFile};
}else if (msa.startsWith("kalign3")){
cmd = "kalign -i " + faiFile + " -o " + faoFile;
cmd = new String[]{"kalign", "-i", faiFile, "-o", faoFile};
}else if (msa.startsWith("kalign")){
cmd = "kalign -gpo 60 -gpe 10 -tgpe 0 -bonus 0 -q -i " + faiFile + " -o " + faoFile;
cmd = new String[]{"kalign", "-gpo", "60", "-gpe", "10", "-tgpe", "0", "-bonus", "0", "-q", "-i", faiFile, "-o", faoFile};
}else if (msa.startsWith("msaprobs")){
cmd = "msaprobs -o " + faoFile + " " + faiFile;
cmd = new String[]{"msaprobs", "-o", faoFile, faiFile};
}else if (msa.startsWith("mafft")){
cmd = "mafft_wrapper.sh " + faiFile + " " + faoFile;
cmd = new String[]{"mafft_wrapper.sh", faiFile, faoFile};
}else{
LOG.error("Unknown msa function " + msa);
throw new InterruptedException("Unknown msa function " + msa);
}

LOG.info("Running " + cmd);
Process process = Runtime.getRuntime().exec(cmd);
LOG.info("Running " + Arrays.toString(cmd));
ProcessBuilder builder = new ProcessBuilder(cmd).redirectErrorStream(true);
if (msa.startsWith("spoa")){
builder.redirectOutput(new File(faoFile));
}
Process process = builder.start();
process.waitFor();
LOG.info("Done " + cmd);
LOG.info("Done " + Arrays.toString(cmd));
temp.deleteOnExit();
}
}

public static Sequence readMSA(String faoFile, int seql) throws IOException{
public static Sequence readPOAOutput(String faoFile, int seql) throws IOException{
SequenceBuilder sb = new SequenceBuilder(Alphabet.DNA(), seql);
BufferedReader bf = FastaReader.openFile(faoFile);
String line = bf.readLine();
Expand All @@ -164,6 +215,20 @@ public static Sequence readMSA(String faoFile, int seql) throws IOException{
LOG.info(sb.getName() + " " + sb.length());
return sb.toSequence();
}
public static Sequence readSPOAOutput(String faoFile, int seql) throws IOException{
SequenceBuilder sb = new SequenceBuilder(Alphabet.DNA(), seql);
BufferedReader bf = FastaReader.openFile(faoFile);
String line = bf.readLine();
while ( (line = bf.readLine()) != null){
if (line.startsWith("Consensus")){
continue;
}//if
sb.append(new Sequence(Alphabet.DNA(), line, "consensus"));
}//while
sb.setName("consensus");
LOG.info(sb.getName() + " " + sb.length());
return sb.toSequence();
}
public static ArrayList<Sequence> readMultipleAlignment(String faoFile) throws IOException{
ArrayList<Sequence> seqList = new ArrayList<Sequence>();
{
Expand Down Expand Up @@ -238,10 +303,12 @@ public static Sequence consensusSequence(List<Sequence> readList, int max, Strin
return null;
}

if ("poa".equals(msa)){
return readMSA(faoFile, readList.get(0).length());

if ("poa".equals(msa))
return readPOAOutput(faoFile, readList.get(0).length());
else if("spoa".equals(msa)){
return readSPOAOutput(faoFile, readList.get(0).length());
}


//3.0 Read in multiple alignment
ArrayList<Sequence> seqList = readMultipleAlignment(faoFile);
Expand Down

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