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* Added DNAse mode; specify the restriction site as "none" to enable * Added exclude fragment flag; use "-x" to run Juicer without creating fragment-delimited maps (this saves 8x space and a lot of time) * Collisions (more than two loci in one read) are now determined and outputted * Added another stage to relaunch at, and updated documentation to make this mode more clear * Added diploid Hi-C creation scripts * Added new flags for easier portability to LSF from AWS/OpenLava * Updated documentation; added version information to output
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| /* | ||
| * The MIT License (MIT) | ||
| * | ||
| * Copyright (c) 2011-2015 Broad Institute, Aiden Lab | ||
| * | ||
| * Permission is hereby granted, free of charge, to any person obtaining a copy | ||
| * of this software and associated documentation files (the "Software"), to deal | ||
| * in the Software without restriction, including without limitation the rights | ||
| * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | ||
| * copies of the Software, and to permit persons to whom the Software is | ||
| * furnished to do so, subject to the following conditions: | ||
| * | ||
| * The above copyright notice and this permission notice shall be included in | ||
| * all copies or substantial portions of the Software. | ||
| * | ||
| * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | ||
| * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | ||
| * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | ||
| * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | ||
| * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | ||
| * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | ||
| * THE SOFTWARE. | ||
| * | ||
| * Based on PicardTools | ||
| * Juicer version 1.5 | ||
| */ | ||
| import java.text.NumberFormat; | ||
| import java.text.ParseException; | ||
| import java.util.Locale; | ||
| import java.io.FileReader; | ||
| import java.io.BufferedReader; | ||
| import java.io.IOException; | ||
| import java.io.File; | ||
| class LibraryComplexity { | ||
| public static void main(String[] args) { | ||
| if (args.length != 2 && args.length != 3 && args.length != 1) { | ||
| System.out.println("Usage: java LibraryComplexity <directory> <output file>"); | ||
| System.out.println(" : java LibraryComplexity <unique> <pcr> <opt>"); | ||
| System.exit(0); | ||
| } | ||
| NumberFormat nf = NumberFormat.getInstance(Locale.US); | ||
|
|
||
| BufferedReader reader = null; | ||
| long readPairs = 0; | ||
| long uniqueReadPairs = 0; | ||
| long opticalDups = 0; | ||
| long totalReadPairs = 0; | ||
| if (args.length == 2 || args.length==1) { | ||
| try { | ||
| File f = new File(args[0] + "/opt_dups.txt"); | ||
| if (f.exists()) { | ||
| reader = new BufferedReader(new FileReader(f)); | ||
| while (reader.readLine() != null) opticalDups++; | ||
| reader.close(); | ||
| } | ||
| f = new File(args[0] + "/merged_nodups.txt"); | ||
| if (f.exists()) { | ||
| reader = new BufferedReader(new FileReader(f)); | ||
| while (reader.readLine() != null) uniqueReadPairs++; | ||
| reader.close(); | ||
| } | ||
| f = new File(args[0] + "/dups.txt"); | ||
| if (f.exists()) { | ||
| reader = new BufferedReader(new FileReader(args[0] + "/dups.txt")); | ||
| while (reader.readLine() != null) readPairs++; | ||
| reader.close(); | ||
| readPairs += uniqueReadPairs; | ||
| } | ||
| String fname = "inter.txt"; | ||
| if (args.length == 2) fname = args[1]; | ||
| f = new File(args[0] + "/" + fname); | ||
| if (f.exists()) { | ||
| reader = new BufferedReader(new FileReader(args[0] + "/" + fname)); | ||
| String line = reader.readLine(); | ||
| boolean done = false; | ||
| while (line != null && !done) { | ||
| if (line.contains("Sequenced Read")) { | ||
| String[] parts = line.split(":"); | ||
| try { | ||
| totalReadPairs = nf.parse(parts[1].trim()).longValue(); | ||
| } | ||
| catch (ParseException e) { | ||
| totalReadPairs = 0; | ||
| } | ||
| done = true; | ||
| } | ||
| line = reader.readLine(); | ||
| } | ||
| reader.close(); | ||
| } | ||
| } catch (IOException error) { | ||
| System.err.println("Problem counting lines in merged_nodups and dups"); | ||
| System.exit(1); | ||
| } | ||
| } | ||
| else { | ||
| try { | ||
| uniqueReadPairs = Integer.valueOf(args[0]); | ||
| readPairs = Integer.valueOf(args[1]); | ||
| opticalDups = Integer.valueOf(args[2]); | ||
| } | ||
| catch (NumberFormatException error) { | ||
| System.err.println("When called with three arguments, must be integers"); | ||
| System.exit(1); | ||
| } | ||
| readPairs += uniqueReadPairs; | ||
| } | ||
| NumberFormat decimalFormat = NumberFormat.getPercentInstance(); | ||
| decimalFormat.setMinimumFractionDigits(2); | ||
| decimalFormat.setMaximumFractionDigits(2); | ||
|
|
||
| long result2 = readPairs*readPairs/(2*(readPairs-uniqueReadPairs)); | ||
|
|
||
| System.out.print("Unique Reads: " + NumberFormat.getInstance().format(uniqueReadPairs) + " "); | ||
| if (totalReadPairs > 0) { | ||
| System.out.println("(" + decimalFormat.format(uniqueReadPairs/(double)totalReadPairs) + ")"); | ||
| } | ||
| else { | ||
| System.out.println(); | ||
| } | ||
|
|
||
| System.out.print("PCR Duplicates: " + nf.format(readPairs - uniqueReadPairs) + " "); | ||
| if (totalReadPairs > 0) { | ||
| System.out.println("(" + decimalFormat.format((readPairs - uniqueReadPairs)/(double)totalReadPairs) + ")"); | ||
| } | ||
| else { | ||
| System.out.println(); | ||
| } | ||
| System.out.print("Optical Duplicates: " + nf.format(opticalDups) + " "); | ||
| if (totalReadPairs > 0) { | ||
| System.out.println("(" + decimalFormat.format(opticalDups/(double)totalReadPairs) + ")"); | ||
| } | ||
| else { | ||
| System.out.println(); | ||
| } | ||
| long result; | ||
| try { | ||
| result = estimateLibrarySize(readPairs, uniqueReadPairs); | ||
| } | ||
| catch (NullPointerException e) { | ||
| System.err.println("Library complexity undefined when total = " + readPairs + " and unique = " + uniqueReadPairs); | ||
| return; | ||
| } | ||
| System.out.println("Library Complexity Estimate: " + nf.format(result)); | ||
| // System.out.println("Library complexity (old): " + nf.format(result2)); | ||
|
|
||
| } | ||
|
|
||
| /** | ||
| * Estimates the size of a library based on the number of paired end molecules | ||
| * observed and the number of unique pairs observed. | ||
| * <br> | ||
| * Based on the Lander-Waterman equation that states:<br> | ||
| * C/X = 1 - exp( -N/X )<br> | ||
| * where<br> | ||
| * X = number of distinct molecules in library<br> | ||
| * N = number of read pairs<br> | ||
| * C = number of distinct fragments observed in read pairs<br> | ||
| */ | ||
| public static Long estimateLibrarySize(final long readPairs, | ||
| final long uniqueReadPairs) { | ||
| final long readPairDuplicates = readPairs - uniqueReadPairs; | ||
|
|
||
| if (readPairs > 0 && readPairDuplicates > 0) { | ||
| long n = readPairs; | ||
| long c = uniqueReadPairs; | ||
|
|
||
| double m = 1.0, M = 100.0; | ||
|
|
||
| if (c >= n || f(m*c, c, n) < 0) { | ||
| throw new IllegalStateException("Invalid values for pairs and unique pairs: " + n + ", " + c); | ||
| } | ||
|
|
||
| while( f(M*c, c, n) >= 0 ) { | ||
| m = M; | ||
| M *= 10.0; | ||
| } | ||
|
|
||
| double r = (m+M)/2.0; | ||
| double u = f( r * c, c, n ); | ||
| int i = 0; | ||
| while (u != 0 && i < 1000) { | ||
| if (u > 0) m = r; | ||
| else M = r; | ||
| r = (m+M)/2.0; | ||
| u = f( r * c, c, n ); | ||
| i++; | ||
| } | ||
| if (i == 1000) { | ||
| System.err.println("Iterated 1000 times, returning estimate"); | ||
| } | ||
|
|
||
| return (long) (c * (m+M)/2.0); | ||
| } | ||
| else { | ||
| return null; | ||
| } | ||
| } | ||
|
|
||
| /** Method that is used in the computation of estimated library size. */ | ||
| private static double f(double x, double c, double n) { | ||
| return c/x - 1 + Math.exp(-n/x); | ||
| } | ||
| } |
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