Mercurial > repos > rliterman > csp2

annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/fileIO/SummaryFile.java @ 68:5028fdace37b

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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 16:23:26 -0400
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jpayne@68 1 package fileIO;
jpayne@68 2
jpayne@68 3 import java.io.File;
jpayne@68 4
jpayne@68 5 import dna.Data;
jpayne@68 6 import shared.Parse;
jpayne@68 7 import shared.PreParser;
jpayne@68 8
jpayne@68 9 /**
jpayne@68 10 * Tests to see if a summary file matches a reference fasta file, based on date, size, and name
jpayne@68 11 * @author Brian Bushnell
jpayne@68 12 * @date Mar 11, 2013
jpayne@68 13 *
jpayne@68 14 */
jpayne@68 15 public class SummaryFile {
jpayne@68 16
jpayne@68 17 public static void main(String[] args){
jpayne@68 18 if(args.length==0){
jpayne@68 19 System.out.println("Usage: SummaryFile <summary file> <reference fasta>");
jpayne@68 20 System.exit(0);
jpayne@68 21 }
jpayne@68 22
jpayne@68 23 {//Preparse block for help, config files, and outstream
jpayne@68 24 PreParser pp=new PreParser(args, new Object() { }.getClass().getEnclosingClass(), false);
jpayne@68 25 args=pp.args;
jpayne@68 26 //outstream=pp.outstream;
jpayne@68 27 }
jpayne@68 28
jpayne@68 29 String summary=null, ref=null;
jpayne@68 30
jpayne@68 31 for(int i=0; i<args.length; i++){
jpayne@68 32
jpayne@68 33 if(args[i].contains("=")){
jpayne@68 34 final String arg=args[i];
jpayne@68 35 final String[] split=arg.split("=");
jpayne@68 36 String a=split[0].toLowerCase();
jpayne@68 37 String b=split.length>1 ? split[1] : null;
jpayne@68 38
jpayne@68 39 if(a.equals("summary")){
jpayne@68 40 summary=b;
jpayne@68 41 }else if(a.equals("ref") || a.equals("reference")){
jpayne@68 42 ref=b;
jpayne@68 43 }else{
jpayne@68 44 throw new RuntimeException("Unknown parameter: "+args[i]);
jpayne@68 45 }
jpayne@68 46
jpayne@68 47 }else{
jpayne@68 48 if(args[i].endsWith("summary.txt")){
jpayne@68 49 summary=args[i];
jpayne@68 50 }else{
jpayne@68 51 ref=args[i];
jpayne@68 52 }
jpayne@68 53 }
jpayne@68 54 }
jpayne@68 55
jpayne@68 56 if(summary==null && args.length>0){
jpayne@68 57 summary=args[0];
jpayne@68 58 }
jpayne@68 59
jpayne@68 60 if(summary==null){
jpayne@68 61 System.out.println("Usage: SummaryFile <summary file> <reference fasta>");
jpayne@68 62 System.exit(0);
jpayne@68 63 }
jpayne@68 64
jpayne@68 65 if(ref==null){
jpayne@68 66
jpayne@68 67 }
jpayne@68 68 }
jpayne@68 69
jpayne@68 70 public boolean compare(final String refName){
jpayne@68 71 try {
jpayne@68 72 File ref=new File(refName);
jpayne@68 73 if(!ref.exists()){
jpayne@68 74 if(refName.startsWith("stdin")){return false;}
jpayne@68 75 else{
jpayne@68 76 assert(false) : "No such file: "+refName;
jpayne@68 77 }
jpayne@68 78 }
jpayne@68 79 // if(!refName.equals(source) && !Files.isSameFile(ref.toPath(), new File(source).toPath())){ //This is Java-7 specific.
jpayne@68 80 //// assert(false) : refName+", "+source+": "+(Files.isSameFile(ref.toPath(), new File(source).toPath()))+
jpayne@68 81 //// "\n"+ref.getCanonicalPath()+", "+new File(source).getCanonicalPath()+": "+(ref.getCanonicalPath().equals(new File(source).getCanonicalPath()));
jpayne@68 82 // return false;
jpayne@68 83 //
jpayne@68 84 // }
jpayne@68 85 if(!refName.equals(source) && !ref.getCanonicalPath().equals(new File(source).getCanonicalPath())){
jpayne@68 86 // assert(false) : refName+", "+source+": "+(Files.isSameFile(ref.toPath(), new File(source).toPath()))+
jpayne@68 87 // "\n"+ref.getCanonicalPath()+", "+new File(source).getCanonicalPath()+": "+(ref.getCanonicalPath().equals(new File(source).getCanonicalPath()));
jpayne@68 88 return false;
jpayne@68 89
jpayne@68 90 }
jpayne@68 91 if(bytes!=ref.length()){
jpayne@68 92 // assert(false) : bytes+", "+ref.length();
jpayne@68 93 return false;
jpayne@68 94 }
jpayne@68 95 if(modified!=ref.lastModified()){
jpayne@68 96 // assert(false) : modified+", "+ref.lastModified();
jpayne@68 97 return false;
jpayne@68 98 }
jpayne@68 99 } catch (Exception e) {
jpayne@68 100 // TODO Auto-generated catch block
jpayne@68 101 e.printStackTrace();
jpayne@68 102 return false;
jpayne@68 103 }
jpayne@68 104 return true;
jpayne@68 105 }
jpayne@68 106
jpayne@68 107 public static boolean compare(final String summaryName, final String refName){
jpayne@68 108 assert(refName!=null) : "Null reference file name.";
jpayne@68 109 if(!new File(summaryName).exists()){
jpayne@68 110 // assert(false);
jpayne@68 111 return false;
jpayne@68 112 }
jpayne@68 113 SummaryFile sf=new SummaryFile(summaryName);
jpayne@68 114 return sf.compare(refName);
jpayne@68 115 }
jpayne@68 116
jpayne@68 117 public static String getName(){
jpayne@68 118 return getName(Data.GENOME_BUILD);
jpayne@68 119 }
jpayne@68 120
jpayne@68 121 public static String getName(int build){
jpayne@68 122 return Data.ROOT_GENOME+build+"/summary.txt";
jpayne@68 123 }
jpayne@68 124
jpayne@68 125 public SummaryFile(String path){
jpayne@68 126 summaryFname=path;
jpayne@68 127 String s;
jpayne@68 128 TextFile tf=new TextFile(summaryFname, false);
jpayne@68 129 for(s=tf.nextLine(); s!=null; s=tf.nextLine()){
jpayne@68 130 if(s.charAt(0)=='#'){
jpayne@68 131 if(s.startsWith("#Version")){
jpayne@68 132 String[] split=s.split("\t");
jpayne@68 133 version=(split.length>1 ? Integer.parseInt(split[1]) : 0);
jpayne@68 134 }
jpayne@68 135 }else{
jpayne@68 136 String[] split=s.split("\t");
jpayne@68 137 String a=split[0];
jpayne@68 138 String b=split[1];
jpayne@68 139 if(a.equalsIgnoreCase("chroms")){chroms=(int)Long.parseLong(b);}
jpayne@68 140 else if(a.equalsIgnoreCase("bases")){bases=Long.parseLong(b);}
jpayne@68 141 else if(a.equalsIgnoreCase("version")){version=Integer.parseInt(b);}
jpayne@68 142 else if(a.equalsIgnoreCase("defined")){definedBases=Long.parseLong(b);}
jpayne@68 143 else if(a.equalsIgnoreCase("contigs")){contigs=Integer.parseInt(b);}
jpayne@68 144 else if(a.equalsIgnoreCase("scaffolds")){scaffolds=Integer.parseInt(b);}
jpayne@68 145 else if(a.equalsIgnoreCase("interpad")){interpad=Integer.parseInt(b);}
jpayne@68 146 else if(a.equalsIgnoreCase("undefined")){undefinedBases=Long.parseLong(b);}
jpayne@68 147 else if(a.equalsIgnoreCase("name")){name=b;}
jpayne@68 148 else if(a.equalsIgnoreCase("source")){source=b;}
jpayne@68 149 else if(a.equalsIgnoreCase("bytes")){bytes=Long.parseLong(b);}
jpayne@68 150 else if(a.equalsIgnoreCase("last modified")){modified=Long.parseLong(b);}
jpayne@68 151 else if(a.equalsIgnoreCase("scafprefixes")){scafprefixes=Parse.parseBoolean(b);}
jpayne@68 152 else{throw new RuntimeException("In file "+tf.name+": Unknown term "+s);}
jpayne@68 153 }
jpayne@68 154 }
jpayne@68 155 tf.close();
jpayne@68 156 }
jpayne@68 157
jpayne@68 158 public final String summaryFname;
jpayne@68 159
jpayne@68 160 public int chroms;
jpayne@68 161 public long contigs;
jpayne@68 162 public long scaffolds;
jpayne@68 163 public int interpad;
jpayne@68 164 public long bases;
jpayne@68 165 public long definedBases;
jpayne@68 166 public long undefinedBases;
jpayne@68 167 public String name;
jpayne@68 168 public String source;
jpayne@68 169 public int version;
jpayne@68 170 public long bytes;
jpayne@68 171 public long modified;
jpayne@68 172 public boolean scafprefixes;
jpayne@68 173
jpayne@68 174 }