2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.analysis;
23 import jalview.datamodel.Alignment;
24 import jalview.datamodel.AlignmentI;
25 import jalview.datamodel.Sequence;
26 import jalview.datamodel.SequenceI;
27 import jalview.io.FastaFile;
30 import java.io.FileNotFoundException;
31 import java.io.PrintStream;
32 import java.util.Arrays;
33 import java.util.Random;
36 * Generates, and outputs in Fasta format, a random peptide or nucleotide alignment for given
37 * sequence length and count. Will regenerate the same alignment each time if
38 * the same random seed is used (so may be used for reproducible unit tests).
39 * Not guaranteed to reproduce the same results between versions, as the rules
40 * may get tweaked to produce more 'realistic' results.
44 public class AlignmentGenerator
46 private static final char GAP = '-';
48 private static final char ZERO = '0';
50 private static final char[] NUCS = "GTCA".toCharArray();
52 private static final char[] PEPS = "MILVFYWHKRDEQNTCGASNP".toCharArray();
54 private static char[] BASES;
56 private Random random;
58 private PrintStream ps;
61 * Outputs a pseudo-randomly generated nucleotide or peptide alignment
64 * <li>n (for nucleotide) or p (for peptide)</li>
65 * <li>length (number of bases in each sequence)</li>
66 * <li>height (number of sequences)</li>
67 * <li>a whole number random seed</li>
68 * <li>percentage of gaps to include (0-100)</li>
69 * <li>percentage chance of variation of each position (0-100)</li>
70 * <li>(optional) path to a file to write the alignment to</li>
75 * @throws FileNotFoundException
77 public static void main(String[] args) throws FileNotFoundException
79 if (args.length != 6 && args.length != 7)
85 PrintStream ps = System.out;
88 ps = new PrintStream(new File(args[6]));
91 boolean nucleotide = args[0].toLowerCase().startsWith("n");
92 int width = Integer.parseInt(args[1]);
93 int height = Integer.parseInt(args[2]);
94 long randomSeed = Long.valueOf(args[3]);
95 int gapPercentage = Integer.valueOf(args[4]);
96 int changePercentage = Integer.valueOf(args[5]);
98 ps.println("; " + height + " sequences of " + width
99 + " bases with " + gapPercentage + "% gaps and "
100 + changePercentage + "% mutations (random seed = " + randomSeed
103 new AlignmentGenerator(nucleotide, ps).generate(width, height,
104 randomSeed, gapPercentage, changePercentage);
106 if (ps != System.out)
113 * Prints parameter help
115 private static void usage()
117 System.out.println("Usage:");
118 System.out.println("arg0: n (for nucleotide) or p (for peptide)");
119 System.out.println("arg1: number of (non-gap) bases per sequence");
120 System.out.println("arg2: number of sequences");
122 .println("arg3: an integer as random seed (same seed = same results)");
123 System.out.println("arg4: percentage of gaps to (randomly) generate");
125 .println("arg5: percentage of 'mutations' to (randomly) generate");
127 .println("arg6: (optional) path to output file (default is sysout)");
128 System.out.println("Example: AlignmentGenerator n 12 15 387 10 5");
130 .println("- 15 nucleotide sequences of 12 bases each, approx 10% gaps and 5% mutations, random seed = 387");
135 * Constructor that sets nucleotide or peptide symbol set, and also writes the
136 * generated alignment to sysout
138 public AlignmentGenerator(boolean nuc)
140 this(nuc, System.out);
144 * Constructor that sets nucleotide or peptide symbol set, and also writes the
145 * generated alignment to the specified output stream (if not null). This can
146 * be used to write the alignment to a file or sysout.
148 public AlignmentGenerator(boolean nucleotide, PrintStream printStream)
150 BASES = nucleotide ? NUCS : PEPS;
155 * Outputs an 'alignment' of given width and height, where each position is a
156 * random choice from the symbol alphabet, or - for gap
161 * @param changePercentage
162 * @param gapPercentage
164 public AlignmentI generate(int width, int height, long randomSeed,
165 int gapPercentage, int changePercentage)
167 SequenceI[] seqs = new SequenceI[height];
168 random = new Random(randomSeed);
169 seqs[0] = generateSequence(1, width, gapPercentage);
170 for (int seqno = 1; seqno < height; seqno++)
172 seqs[seqno] = generateAnotherSequence(seqs[0].getSequence(),
173 seqno + 1, width, changePercentage);
175 AlignmentI al = new Alignment(seqs);
179 ps.println(new FastaFile().print(al.getSequencesArray(), true));
186 * Outputs a DNA 'sequence' of given length, with some random gaps included.
190 * @param gapPercentage
192 private SequenceI generateSequence(int seqno, int length,
195 StringBuilder seq = new StringBuilder(length);
198 * Loop till we've added 'length' bases (excluding gaps)
200 for (int count = 0; count < length;)
202 boolean addGap = random.nextInt(100) < gapPercentage;
203 char c = addGap ? GAP : BASES[random.nextInt(Integer.MAX_VALUE)
211 final String seqName = "SEQ" + seqno;
212 final String seqString = seq.toString();
213 SequenceI sq = new Sequence(seqName, seqString);
214 sq.createDatasetSequence();
219 * Generate a sequence approximately aligned to the first one.
225 * @param changePercentage
228 private SequenceI generateAnotherSequence(char[] ds, int seqno,
229 int width, int changePercentage)
231 int length = ds.length;
232 char[] seq = new char[length];
233 Arrays.fill(seq, ZERO);
234 int gapsWanted = length - width;
238 * First 'randomly' mimic gaps in model sequence.
240 for (int pos = 0; pos < length; pos++)
245 * Add a gap at the same position with changePercentage likelihood
247 seq[pos] = randomCharacter(GAP, changePercentage);
256 * Next scatter any remaining gaps (if any) at random. This gives an even
259 while (gapsAdded < gapsWanted)
261 boolean added = false;
264 int pos = random.nextInt(length);
275 * Finally fill in the rest with randomly mutated bases.
277 for (int pos = 0; pos < length; pos++)
279 if (seq[pos] == ZERO)
281 char c = randomCharacter(ds[pos], changePercentage);
285 final String seqName = "SEQ" + seqno;
286 final String seqString = new String(seq);
287 SequenceI sq = new Sequence(seqName, seqString);
288 sq.createDatasetSequence();
293 * Returns a random character that is changePercentage% likely to match the
294 * given type (as base or gap).
296 * @param changePercentage
301 private char randomCharacter(char c, int changePercentage)
303 final boolean mutation = random.nextInt(100) < changePercentage;
313 newchar = BASES[random.nextInt(Integer.MAX_VALUE) % BASES.length];