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package fileIO;
import java.io.File;
import dna.Data;
import shared.Parse;
import shared.PreParser;
/**
* Tests to see if a summary file matches a reference fasta file, based on date, size, and name
* @author Brian Bushnell
* @date Mar 11, 2013
*
*/
public class SummaryFile {
public static void main(String[] args){
if(args.length==0){
System.out.println("Usage: SummaryFile <summary file> <reference fasta>");
System.exit(0);
}
{//Preparse block for help, config files, and outstream
PreParser pp=new PreParser(args, new Object() { }.getClass().getEnclosingClass(), false);
args=pp.args;
//outstream=pp.outstream;
}
String summary=null, ref=null;
for(int i=0; i<args.length; i++){
if(args[i].contains("=")){
final String arg=args[i];
final String[] split=arg.split("=");
String a=split[0].toLowerCase();
String b=split.length>1 ? split[1] : null;
if(a.equals("summary")){
summary=b;
}else if(a.equals("ref") || a.equals("reference")){
ref=b;
}else{
throw new RuntimeException("Unknown parameter: "+args[i]);
}
}else{
if(args[i].endsWith("summary.txt")){
summary=args[i];
}else{
ref=args[i];
}
}
}
if(summary==null && args.length>0){
summary=args[0];
}
if(summary==null){
System.out.println("Usage: SummaryFile <summary file> <reference fasta>");
System.exit(0);
}
if(ref==null){
}
}
public boolean compare(final String refName){
try {
File ref=new File(refName);
if(!ref.exists()){
if(refName.startsWith("stdin")){return false;}
else{
assert(false) : "No such file: "+refName;
}
}
// if(!refName.equals(source) && !Files.isSameFile(ref.toPath(), new File(source).toPath())){ //This is Java-7 specific.
//// assert(false) : refName+", "+source+": "+(Files.isSameFile(ref.toPath(), new File(source).toPath()))+
//// "\n"+ref.getCanonicalPath()+", "+new File(source).getCanonicalPath()+": "+(ref.getCanonicalPath().equals(new File(source).getCanonicalPath()));
// return false;
//
// }
if(!refName.equals(source) && !ref.getCanonicalPath().equals(new File(source).getCanonicalPath())){
// assert(false) : refName+", "+source+": "+(Files.isSameFile(ref.toPath(), new File(source).toPath()))+
// "\n"+ref.getCanonicalPath()+", "+new File(source).getCanonicalPath()+": "+(ref.getCanonicalPath().equals(new File(source).getCanonicalPath()));
return false;
}
if(bytes!=ref.length()){
// assert(false) : bytes+", "+ref.length();
return false;
}
if(modified!=ref.lastModified()){
// assert(false) : modified+", "+ref.lastModified();
return false;
}
} catch (Exception e) {
// TODO Auto-generated catch block
e.printStackTrace();
return false;
}
return true;
}
public static boolean compare(final String summaryName, final String refName){
assert(refName!=null) : "Null reference file name.";
if(!new File(summaryName).exists()){
// assert(false);
return false;
}
SummaryFile sf=new SummaryFile(summaryName);
return sf.compare(refName);
}
public static String getName(){
return getName(Data.GENOME_BUILD);
}
public static String getName(int build){
return Data.ROOT_GENOME+build+"/summary.txt";
}
public SummaryFile(String path){
summaryFname=path;
String s;
TextFile tf=new TextFile(summaryFname, false);
for(s=tf.nextLine(); s!=null; s=tf.nextLine()){
if(s.charAt(0)=='#'){
if(s.startsWith("#Version")){
String[] split=s.split("\t");
version=(split.length>1 ? Integer.parseInt(split[1]) : 0);
}
}else{
String[] split=s.split("\t");
String a=split[0];
String b=split[1];
if(a.equalsIgnoreCase("chroms")){chroms=(int)Long.parseLong(b);}
else if(a.equalsIgnoreCase("bases")){bases=Long.parseLong(b);}
else if(a.equalsIgnoreCase("version")){version=Integer.parseInt(b);}
else if(a.equalsIgnoreCase("defined")){definedBases=Long.parseLong(b);}
else if(a.equalsIgnoreCase("contigs")){contigs=Integer.parseInt(b);}
else if(a.equalsIgnoreCase("scaffolds")){scaffolds=Integer.parseInt(b);}
else if(a.equalsIgnoreCase("interpad")){interpad=Integer.parseInt(b);}
else if(a.equalsIgnoreCase("undefined")){undefinedBases=Long.parseLong(b);}
else if(a.equalsIgnoreCase("name")){name=b;}
else if(a.equalsIgnoreCase("source")){source=b;}
else if(a.equalsIgnoreCase("bytes")){bytes=Long.parseLong(b);}
else if(a.equalsIgnoreCase("last modified")){modified=Long.parseLong(b);}
else if(a.equalsIgnoreCase("scafprefixes")){scafprefixes=Parse.parseBoolean(b);}
else{throw new RuntimeException("In file "+tf.name+": Unknown term "+s);}
}
}
tf.close();
}
public final String summaryFname;
public int chroms;
public long contigs;
public long scaffolds;
public int interpad;
public long bases;
public long definedBases;
public long undefinedBases;
public String name;
public String source;
public int version;
public long bytes;
public long modified;
public boolean scafprefixes;
}
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