2 package org.forester.application;
5 import java.io.FileInputStream;
6 import java.util.ArrayList;
9 import org.forester.io.parsers.FastaParser;
10 import org.forester.io.parsers.GeneralMsaParser;
11 import org.forester.msa.Msa;
12 import org.forester.msa.MsaCompactor;
13 import org.forester.msa.MsaMethods;
14 import org.forester.util.CommandLineArguments;
15 import org.forester.util.ForesterUtil;
17 public class msa_compactor {
19 final static private String HELP_OPTION_1 = "help";
20 final static private String HELP_OPTION_2 = "h";
21 final static private String REMOVE_WORST_OFFENDERS_OPTION = "w";
22 final static private String AV_GAPINESS_OPTION = "a";
23 final static private String STEP_OPTION = "s";
24 final static private String LENGTH_OPTION = "l";
25 final static private String REALIGN_OPTION = "r";
26 final static private String PRG_NAME = "msa_compactor";
27 final static private String PRG_DESC = "multiple sequnce aligment compactor";
28 final static private String PRG_VERSION = "0.90";
29 final static private String PRG_DATE = "2012.07.13";
30 final static private String E_MAIL = "phylosoft@gmail.com";
31 final static private String WWW = "www.phylosoft.org/forester/";
33 public static void main( final String args[] ) {
35 final CommandLineArguments cla = new CommandLineArguments( args );
36 if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) || ( cla.getNumberOfNames() != 2 ) ) {
40 final File in = cla.getFile( 0 );
41 final File out = cla.getFile( 1 );
42 int worst_remove = -1;
46 boolean realign = false;
47 final List<String> allowed_options = new ArrayList<String>();
48 allowed_options.add( REMOVE_WORST_OFFENDERS_OPTION );
49 allowed_options.add( AV_GAPINESS_OPTION );
50 allowed_options.add( LENGTH_OPTION );
51 allowed_options.add( REALIGN_OPTION );
52 allowed_options.add( STEP_OPTION );
53 final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
54 if ( dissallowed_options.length() > 0 ) {
55 ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );
57 if ( cla.isOptionSet( REMOVE_WORST_OFFENDERS_OPTION ) ) {
58 worst_remove = cla.getOptionValueAsInt( REMOVE_WORST_OFFENDERS_OPTION );
60 if ( cla.isOptionSet( AV_GAPINESS_OPTION ) ) {
61 av = cla.getOptionValueAsDouble( AV_GAPINESS_OPTION );
63 if ( cla.isOptionSet( LENGTH_OPTION ) ) {
64 length = cla.getOptionValueAsInt( LENGTH_OPTION );
66 if ( cla.isOptionSet( STEP_OPTION ) ) {
67 step = cla.getOptionValueAsInt( STEP_OPTION );
69 if ( cla.isOptionSet( REALIGN_OPTION ) ) {
72 // else if ( cla.isOptionSet( STEP_OPTION ) && cla.isOptionSet( WINDOW_OPTION ) ) {
73 // step = cla.getOptionValueAsInt( STEP_OPTION );
74 // window = cla.getOptionValueAsInt( WINDOW_OPTION );
81 final FileInputStream is = new FileInputStream( in );
82 if ( FastaParser.isLikelyFasta( in ) ) {
83 msa = FastaParser.parseMsa( is );
86 msa = GeneralMsaParser.parse( is );
88 MsaCompactor mc = null;
89 if ( worst_remove > 0 ) {
90 mc = MsaCompactor.removeWorstOffenders( msa, worst_remove, realign );
93 mc = MsaCompactor.reduceGapAverage( msa, av, step, realign, out, 50 );
95 else if ( length > 0 ) {
96 mc = MsaCompactor.reduceLength( msa, length, step, realign );
98 System.out.println( MsaMethods.calcGapRatio( mc.getMsa() ) );
99 for( final String id : mc.getRemovedSeqIds() ) {
100 System.out.println( id );
103 catch ( final Exception e ) {
105 ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
109 private static void printHelp() {
110 ForesterUtil.printProgramInformation( PRG_NAME,
116 ForesterUtil.getForesterLibraryInformation() );
117 System.out.println( "Usage:" );
118 System.out.println();
119 System.out.println( PRG_NAME + " <options> <msa input file>" );
120 System.out.println();
121 System.out.println( " options: " );
122 System.out.println();
123 // System.out.println( " -" + FROM_OPTION + "=<integer>: from (msa column)" );
124 // System.out.println( " -" + TO_OPTION + "=<integer>: to (msa column)" );
125 // System.out.println( " or" );
126 // System.out.println( " -" + WINDOW_OPTION + "=<integer>: window size (msa columns)" );
127 System.out.println( " -" + REMOVE_WORST_OFFENDERS_OPTION + "=<integer>: step size (msa columns)" );
128 System.out.println();
129 System.out.println();
130 System.out.println();