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package align2;
import java.util.ArrayList;
import java.util.Arrays;
import fileIO.TextFile;
import shared.Tools;
public class ReformatBatchOutput {
// Elapsed: 31.7
//
// Mapping Statistics for 0s_default.sam:
// mapped: 100.00%
// retained: 96.06%
// discarded: 0.00%
// ambiguous: 3.94%
//
// Strict correctness (both ends exactly correct):
// true positive: 96.06%
// false positive: 0.00%
//
// Loose correctness (one end approximately correct):
// true positive: 96.06%
// false positive: 0.00%
//
// false negative: 0.00%
// Elapsed: 2.34
// Elapsed: 20.51
// Elapsed: 0.33
//
// Mapping Statistics for bwa_0S_0I_0D_0U_0N_r100.sam:
// primary alignments: 100 found of 100 expected
// secondary alignments: 0 found
// mapped: 100.000%
// retained: 97.000%
// discarded: 0.000%
// ambiguous: 3.000%
//
// Strict correctness (both ends exactly correct):
// true positive: 97.000%
// false positive: 0.000%
//
// Loose correctness (one end approximately correct):
// true positive: 97.000%
// false positive: 0.000%
//
// false negative: 0.000%
public static void main(String[] args){
TextFile tf=new TextFile(args[0], false);
String[] lines=tf.toStringLines();
ArrayList<String> list=new ArrayList<String>();
int mode=0;
System.out.println(header());
for(String s : lines){
if(s.startsWith("Elapsed:")){
if(!list.isEmpty()){
process(list); //failure
list.clear();
mode=0;
}
mode++;
}
if(mode>0){
list.add(s);
if(s.startsWith("false negative:")){
process(list);
list.clear();
mode=0;
}
}
}
}
public static String header() {
return("program\tfile\tvartype\tcount\treads\tprimary\tsecondary\ttime\tmapped\tretained\tdiscarded\tambiguous\ttruePositive\t" +
"falsePositive\ttruePositiveL\tfalsePositiveL\tfalseNegative");
}
//bwa_1S_0I_0D_0U_0N_r400000x100.sam
public static int getReads(String name){
// String[] split=name.substring(0, name.length()-4).split("_");
String[] split=name.split("_");
String r=(split[split.length-1]);
if(r.charAt(0)=='r' && Tools.isDigit(r.charAt(r.length()-1))){
assert(r.charAt(0)=='r') : Arrays.toString(split)+", "+name;
r=r.substring(1);
if(r.contains("x")){
r=r.substring(0, r.indexOf('x'));
}
return Integer.parseInt(r);
}else{
for(String s : split){
if(s.endsWith("bp") && s.contains("x") && Tools.isDigit(s.charAt(0))){
r=s.substring(0, s.indexOf('x')-1);
return Integer.parseInt(r);
}
}
}
return 0;
}
public static char getVarType(String name){
// String[] split=name.substring(0, name.length()-4).split("_");
String[] split=name.split("_");
for(String s : split){
char c=s.charAt(0);
if(Tools.isDigit(c) && c!='0' && !s.endsWith("bp")){
return s.charAt(s.length()-1);
}
}
return '?';
}
public static int getCount(String name){
// String[] split=name.substring(0, name.length()-4).split("_");
String[] split=name.split("_");
for(String s : split){
char c=s.charAt(0);
if(Tools.isDigit(c) && c!='0' && !s.endsWith("bp")){
String r=s.substring(0, s.length()-1);
return Integer.parseInt(r);
}
}
return 0;
}
public static String getProgram(String name){
return name.substring(0, name.indexOf('_'));
}
public static void process(ArrayList<String> list){
String name=null;
// String count=null;
String time=null;
StringBuilder sb=new StringBuilder();
int primary=0;
int secondary=0;
int expected=0;
for(String s : list){
String[] split=s.split("\t");
String a=split[0];
String b=split.length>1 ? split[1] : null;
if(a.equals("Elapsed:")){
time=b;
}else if(a.startsWith("lines:")){
//do nothing
}else if(a.startsWith("Mapping Statistics for ")){
name=a.replace("Mapping Statistics for ", "").replace(".sam:", "");
}else if(a.startsWith("primary alignments:")){
assert(b!=null) : "Bad line: "+s;
b=b.replace(" found of ", "_");
b=b.replace(" expected", "");
String[] split2=b.split("_");
primary=Integer.parseInt(split2[0]);
expected=Integer.parseInt(split2[1]);
}else if(a.startsWith("secondary alignments:")){
assert(b!=null) : "Bad line: "+s;
b=b.replace(" found", "");
secondary=Integer.parseInt(b);
}else if(b!=null){
assert(!b.contains("found")) : "\na='"+a+"'\nb='"+b+"'\n"+a.equals("primary alignments:");
sb.append('\t').append(b.replace("%", ""));
}
}
// if(name!=null){
// count="";
//
// String[] split=name.split("_");
//
// for(String s : split){
// if(s!=null && s.length()>0 && s.charAt(0)!='0'){
// for(int i=0; i<s.length(); i++){
// char c=s.charAt(i);
// if(Tools.isDigit(c)){count=count+c;}
// else{break;}
// }
// }
// if(count.length()>0){break;}
// }
// }
String prg=null;
char type='S';
int reads=1;
int vars=0;
if(name!=null){
try {
prg=getProgram(name);
type=getVarType(name);
reads=getReads(name);
vars=getCount(name);
} catch (Exception e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
System.out.println(prg+"\t"+name+"\t"+type+"\t"+vars+"\t"+reads+"\t"+primary+"\t"+secondary+"\t"+time+sb);
}
}
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