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org.forester.application.sdi_dir Maven / Gradle / Ivy
Applications and software libraries for evolutionary biology and comparative genomics research
// $Id:
// FORESTER -- software libraries and applications
// for evolutionary biology research and applications.
//
// Copyright (C) 2008-2009 Christian M. Zmasek
// Copyright (C) 2008-2009 Burnham Institute for Medical Research
// Copyright (C) 2000-2001 Washington University School of Medicine
// and Howard Hughes Medical Institute
// All rights reserved
//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// version 2.1 of the License, or (at your option) any later version.
//
// This library is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
// WWW: www.phylosoft.org/forester
package org.forester.application;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.io.PrintWriter;
import java.util.Arrays;
import org.forester.io.parsers.phyloxml.PhyloXmlParser;
import org.forester.io.writers.PhylogenyWriter;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.sdi.SDIException;
import org.forester.sdi.SDIR;
import org.forester.sdi.SDIse;
import org.forester.util.ForesterUtil;
/*
* Allows to infer duplications - speciations on all (rooted or unrooted) gene
* trees in a directory by using method "infer" of class SDIunrooted. The
* output of this is a (re)rooted tree with speciation - duplication assigned
* for each tree (in "gene tree directory" with suffix "suffix for gene trees"),
* as well as a summary list ("outputfile name").
The summary list contains
* the following. The number in brackets indicates how many external nodes of
* the gene tree had to be removed since the associated species was not found in
* the species tree. "en" indicates the number of external nodes in the
* resulting (analyzed and returned) gene tree. "d" are the number of
* duplications, "L=" the mapping cost, "h=" the height, "d=" the minimal
* difference in tree heights (of the two subtrees at the root; this number is
* 0.0 for a midpoint rooted tree) of the resulting, analyzed and rooted gene
* tree(s).
The output file ending with "_Sdist" is a file which lists the
* distribution of trees sizes, "_Ddist" lists the distribution of the sums of
* duplications (up to a certain maximal size, set with final variables
* MAX_EXT_NODE_DIST and MAX_DUP_DIST).
*
* @see SDIunrooted
*
* @author Christian M. Zmasek
*/
public class sdi_dir {
final static private String E_MAIL = "[email protected] ";
final static private String WWW = "www.phylosoft.org";
final static private String PRG_NAME = "sdi_dir";
final static private String PRG_VERSION = "2.00";
final static private String PRG_DATE = "2010.04.26";
private static void errorInCommandLine() {
System.out.println( "\nsdi_dir: Error in command line.\n" );
System.out.print( "Usage: % sdi_dir [-options] " );
System.out.println( " " );
System.out.println( "\nOptions:" );
System.out.println( " -l to root by minimizing the mapping cost L (and also the sum of duplications)" );
System.out.println( " -d to root by minimizing the sum of duplications" );
System.out.println( " -h to root by minimizing tree height (can be used together with -l or -d)" );
System.out.println( " -w to write assigned gene trees into output directory" );
System.out.println( "\nGene tree directory" );
System.out.println( " The directory from which to read phyloXML formatted gene trees which" );
System.out.println( " contain taxonomic information in appropriate sub-elements of taxonomy" );
System.out.println( " (see: www.phyloxml.org)." );
System.out.println( " The gene trees can either be rooted, in which case no rooting with -l, -d, or -h " );
System.out.println( " is necessary, or they can be unrooted, in which case rooting is mandatory." );
System.out.println( "\nSuffix for gene trees" );
System.out.println( " Suffix of the gene trees to analyze (e.g. \".phyloxml\")." );
System.out.println( "\nSpecies tree file" );
System.out.println( " In phyloXML format, taxonomic information in appropriate sub-elements of taxonomy." );
System.out.println( " (see: www.phyloxml.org)." );
System.out.println( "\nOutput directory" );
System.out.println( " The directory into which the assigned gene trees will be written." );
System.out.println( "\nOutputfile name" );
System.out.println( " File name for summary output files." );
System.out.println( "" );
System.exit( -1 );
}
/**
* Runs method "infer" of class SDIunrooted on all gene trees in directory
* indir.
*
* Trees are rooted by minimizing either the sum of duplications, the
* mapping cost L, or the tree height (or combinations thereof). One
* resulting tree for each (out of possibly many) is stored in outdir and a
* summary outfile is created. The distributions of the tree sizes (name of
* outfile + _Ddist) and the distributions of the sum of duplications per
* tree (name of outfile + _Sdist) are written out as well.
*
* If both minimize_sum_of_dup and minimize_mapping_cost are true, trees are
* rooted by minimizing by minimizing the mapping cost L.
*
* If minimize_sum_of_dup, minimize_mapping_cost, and minimize_height are
* false trees are assumed to be alreadty rooted.
*
* (Last modified: 02/02/01)
*
* @see SDIR#infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
* @param indir
* a directory containing gene trees in NHX format
* @param species_tree_file
* a species tree file in NHX format
* @param outdir
* a directory where to write trees
* @param outfile
* a file name for the summary file
* @param suffix
* a suffix for the trees to read (e.g. nhx), is case sensitive
* @param write_trees
* set to true to write out one tree with minmal duplications or
* L each
* @param minimize_mapping_cost
* set to true to root by minimizing the mapping cost L
* @param minimize_sum_of_dup
* set to true to root by minimizing the sum of duplications
* @param minimize_height
* set to true to root by minimizing the tree height -- if
* minimize_mapping_cost is set to true or minimize_sum_of_dup is
* set to true, then out of the resulting trees with minimal
* mapping cost or minimal number of duplications the tree with
* the minimal height is chosen
* @throws SDIException
*/
public static void infer( final File indir,
final File species_tree_file,
final File outdir,
final File outfile,
String suffix,
final boolean write_trees,
final boolean minimize_mapping_cost,
boolean minimize_sum_of_dup,
final boolean minimize_height ) throws IOException, SDIException {
final int MIN_EXT_NODES = 4; // Minimal size of trees [in ext nodes]
// to be analyzed.
final int MAX_EXT_NODES = 5000; // Maximal size of trees [in ext nodes]
// to be analyzed.
final int MAX_DUP_DIST = 50; // Max number of dups to output in dup
// distribution ("_Ddist").
final int MAX_EXT_NODE_DIST = 1000; // Max number of ext nodes to output
// in size
// distribution ("_Sdist").
int successful = 0, number_of_too_small_trees = 0, number_of_too_large_trees = 0, dups = 0, c = 0, ext_nodes = 0, removed = 0;
final int nodecount0 = 0;
int j = 0;
long total_number_of_d = 0, total_number_of_ext_nodes = 0, sum_costs = 0;
double sum_tree_heights = 0.0, sum_subtree_diff = 0.0;
Phylogeny species_tree = null;
String filename = null;
String[] filenames = null;
Phylogeny[] trees = null;
final int[] duplications = new int[ MAX_EXT_NODES - 1 ], // For dup
// distribution.
sizes = new int[ MAX_EXT_NODES - 1 ]; // For ext nodes dist.of
// successfully assigned trees.
File outtree = null;
PrintWriter out = null, out_ddist = null, out_sdist = null;
final File ddist_outfile = new File( outfile + "_Ddist" ), sdist_outfile = new File( outfile + "_Sdist" );
final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.0#####" );
df.setDecimalSeparatorAlwaysShown( true );
if ( !indir.exists() || !indir.isDirectory() ) {
throw new IllegalArgumentException( indir + " does not exist or is not a directory." );
}
if ( !outdir.exists() || !outdir.isDirectory() ) {
throw new IllegalArgumentException( outdir + " does not exist or is not a directory." );
}
if ( outfile.exists() ) {
throw new IllegalArgumentException( outfile + " does already exist." );
}
if ( ddist_outfile.exists() ) {
throw new IllegalArgumentException( ddist_outfile + " does already exist." );
}
if ( sdist_outfile.exists() ) {
throw new IllegalArgumentException( sdist_outfile + " does already exist." );
}
if ( !species_tree_file.exists() || !species_tree_file.isFile() ) {
throw new IllegalArgumentException( species_tree_file + " does not exist or is not a file." );
}
if ( minimize_mapping_cost && minimize_sum_of_dup ) {
minimize_sum_of_dup = false;
}
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
species_tree = factory.create( species_tree_file, new PhyloXmlParser() )[ 0 ];
filenames = indir.list();
Arrays.sort( filenames );
suffix = suffix.trim();
out = new PrintWriter( new FileWriter( outfile ), true );
//nodecount0 = PhylogenyNode.getNodeCount();
for( int i = 0; i < filenames.length; ++i ) {
filename = filenames[ i ];
if ( ( suffix.length() < 1 ) || filename.endsWith( suffix ) ) {
final File gene_tree_file = new File( indir.getPath(), filename );
if ( gene_tree_file.exists() && gene_tree_file.isFile() ) {
out.print( j + "\t" + filename );
System.out.println( j + ": " + filename );
j++;
Phylogeny gene_tree = null;
gene_tree = factory.create( gene_tree_file, new PhyloXmlParser() )[ 0 ];
// Removes from gene_tree all species not found in
// species_tree.
removed = PhylogenyMethods.taxonomyBasedDeletionOfExternalNodes( species_tree, gene_tree );
if ( filename.length() < 8 ) {
out.print( "\t\t\t[-" + removed + "]" );
}
else if ( filename.length() < 16 ) {
out.print( "\t\t[-" + removed + "]" );
}
else {
out.print( "\t[-" + removed + "]" );
}
if ( gene_tree.getNumberOfExternalNodes() < MIN_EXT_NODES ) {
out.print( "\t<" + MIN_EXT_NODES + "en\n" );
number_of_too_small_trees++;
}
else if ( gene_tree.getNumberOfExternalNodes() > MAX_EXT_NODES ) {
out.print( "\t>" + MAX_EXT_NODES + "en\n" );
number_of_too_large_trees++;
}
else {
SDIR sdiunrooted = null;
// PhylogenyNode.setNodeCount( nodecount0 );
sdiunrooted = new SDIR();
if ( minimize_mapping_cost || minimize_sum_of_dup || minimize_height ) {
trees = sdiunrooted.infer( gene_tree,
species_tree,
minimize_mapping_cost,
minimize_sum_of_dup,
minimize_height,
write_trees,
1 );
dups = sdiunrooted.getMinimalDuplications();
}
else {
final SDIse sdi = new SDIse( gene_tree, species_tree );
trees = new Phylogeny[ 1 ];
trees[ 0 ] = gene_tree;
dups = sdi.getDuplicationsSum();
c = sdi.computeMappingCostL();
sum_costs += c;
out.print( "\t L=" + c );
}
successful++;
ext_nodes = gene_tree.getNumberOfExternalNodes();
total_number_of_ext_nodes += ext_nodes;
sizes[ ext_nodes ]++;
out.print( "\t " + ext_nodes + "en" );
total_number_of_d += dups;
duplications[ dups ]++;
out.print( "\t " + dups + "d" );
if ( minimize_mapping_cost ) {
c = sdiunrooted.getMinimalMappingCost();
sum_costs += c;
out.print( "\t L=" + c );
}
if ( minimize_height ) {
out.print( "\t h=" + df.format( sdiunrooted.getMinimalTreeHeight() ) );
out.print( "\t d=" + df.format( sdiunrooted.getMinimalDiffInSubTreeHeights() ) );
sum_tree_heights += sdiunrooted.getMinimalTreeHeight();
sum_subtree_diff += sdiunrooted.getMinimalDiffInSubTreeHeights();
}
out.println();
if ( write_trees ) {
outtree = new File( outdir, new File( filenames[ i ] ).getName() );
final PhylogenyWriter writer = new PhylogenyWriter();
writer.toPhyloXML( outtree, trees[ 0 ], 1 );
}
}
}
}
}
//PhylogenyNode.setNodeCount( nodecount0 );
if ( minimize_mapping_cost ) {
out.println( "\nRooted by minimizing mapping cost L." );
System.out.println( "\nRooted by minimizing mapping cost L." );
if ( minimize_height ) {
out.println( "Selected tree(s) with minimal height out of resulting trees." );
System.out.println( "Selected tree(s) with minimal height out of resulting trees." );
}
}
else if ( minimize_sum_of_dup ) {
out.println( "\nRooted by minimizing sum of duplications." );
System.out.println( "\nRooted by minimizing sum of duplications." );
if ( minimize_height ) {
out.println( "Selected tree(s) with minimal height out of resulting trees." );
System.out.println( "Selected tree(s) with minimal height out of resulting trees." );
}
}
else if ( minimize_height ) {
out.println( "\nRooted by minimizing tree height." );
System.out.println( "\nRooted by minimizing tree height." );
}
else {
out.println( "\nNo (re) rooting was performed." );
System.out.println( "\nNo (re) rooting was performed." );
}
out.println( "\nTrees directory : " + indir );
out.println( "Suffix for trees : " + suffix );
out.println( "Species tree : " + species_tree_file );
out.println( "Output directory : " + outdir );
out.println( "Output file : " + outfile );
out.println( "\nTotal number of attempts (tree files read) : " + j );
out.println( "Total number of successfully assigned trees : " + successful );
out.println( "Number of too small trees : " + number_of_too_small_trees );
out.println( "Number of too large trees : " + number_of_too_large_trees );
out.println( "\nSum of duplications : " + total_number_of_d );
if ( minimize_mapping_cost ) {
out.println( "Sum of mapping costs L : " + sum_costs );
}
if ( minimize_height ) {
out.println( "Sum of tree heights : " + sum_tree_heights );
out.println( "Sum of differences in subtree heights : " + sum_subtree_diff );
}
out.println( "Sum of external nodes (in successfully assigned trees): " + total_number_of_ext_nodes );
out.close();
System.out.println( "\nTotal number of attempts (tree files read) : " + j );
System.out.println( "Total number of successfully assigned trees : " + successful );
System.out.println( "Number of too small trees : " + number_of_too_small_trees );
System.out.println( "Number of too large trees : " + number_of_too_large_trees );
System.out.println( "\nSum of duplications : " + total_number_of_d );
if ( minimize_mapping_cost ) {
System.out.println( "Sum of mapping costs L : " + sum_costs );
}
if ( minimize_height ) {
System.out.println( "Sum of tree heights : " + sum_tree_heights );
System.out.println( "Sum of differences in subtree heights : " + sum_subtree_diff );
}
System.out.println( "Sum of external nodes (in successfully assigned trees): " + total_number_of_ext_nodes );
out_ddist = new PrintWriter( new FileWriter( ddist_outfile ), true );
for( int i = 0; ( i < duplications.length ) && ( i <= MAX_DUP_DIST ); ++i ) {
out_ddist.println( i + " " + duplications[ i ] );
}
out_ddist.close();
out_sdist = new PrintWriter( new FileWriter( sdist_outfile ), true );
for( int i = 0; ( i < sizes.length ) && ( i <= MAX_EXT_NODE_DIST ); ++i ) {
out_sdist.println( i + " " + sizes[ i ] );
}
out_sdist.close();
} // infer
/**
* Main method for this class.
*
* (Last modified: 04/26/10)
*
* @param [args[0]
* -l to root by minimizing mapping cost L]
* @param [args[0]
* -d to root by minimizing sum of duplications]
* @param [args[0]
* -w to write out trees into outdir]
* @param [args[0]
* -h to root by minimizing tree height]
* @param [args[0]
* -n input trees are in New Hampshire format instead of NHX --
* or gene tree is in NHX, but species information in gene tree
* is only present in the form of SWISS-PROT sequence names]
* @param args[0or1]
* trees directory name
* @param args[1or2]
* suffix for gene trees
* @param args[2or3]
* speciestree file name
* @param args[3or4]
* output directory name
* @param args[4or5]
* output file name
*/
public static void main( final String args[] ) {
ForesterUtil.printProgramInformation( PRG_NAME, PRG_VERSION, PRG_DATE, E_MAIL, WWW );
// These are the default values.
boolean minimize_mapping_cost = false;
boolean minimize_sum_of_dup = false;
boolean minimize_height = false;
boolean write_trees = false;
File indir = null;
File speciestree_file = null;
File outdir = null;
File outfile = null;
String suffix = null;
if ( args.length == 5 ) {
indir = new File( args[ 0 ] );
suffix = args[ 1 ];
speciestree_file = new File( args[ 2 ] );
outdir = new File( args[ 3 ] );
outfile = new File( args[ 4 ] );
}
else if ( args.length == 6 ) {
if ( args[ 0 ].startsWith( "-" ) ) {
minimize_mapping_cost = false;
minimize_sum_of_dup = false;
minimize_height = false;
write_trees = false;
if ( args[ 0 ].toLowerCase().indexOf( "w" ) != -1 ) {
write_trees = true;
}
if ( args[ 0 ].toLowerCase().indexOf( "l" ) != -1 ) {
minimize_mapping_cost = true;
}
if ( args[ 0 ].toLowerCase().indexOf( "d" ) != -1 ) {
minimize_sum_of_dup = true;
}
if ( args[ 0 ].toLowerCase().indexOf( "h" ) != -1 ) {
minimize_height = true;
}
}
else {
sdi_dir.errorInCommandLine();
}
indir = new File( args[ 1 ] );
suffix = args[ 2 ];
speciestree_file = new File( args[ 3 ] );
outdir = new File( args[ 4 ] );
outfile = new File( args[ 5 ] );
}
else {
sdi_dir.errorInCommandLine();
}
if ( minimize_mapping_cost && minimize_sum_of_dup ) {
minimize_sum_of_dup = false;
}
try {
sdi_dir.infer( indir,
speciestree_file,
outdir,
outfile,
suffix,
write_trees,
minimize_mapping_cost,
minimize_sum_of_dup,
minimize_height );
}
catch ( final Exception e ) {
ForesterUtil.fatalError( PRG_NAME, "error: " + e.getLocalizedMessage() );
}
ForesterUtil.programMessage( PRG_NAME, "OK." );
}
}
