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.Msa.MSA_FORMAT;
13 import org.forester.msa.MsaMethods;
14 import org.forester.msa_compactor.MsaCompactor;
15 import org.forester.util.CommandLineArguments;
16 import org.forester.util.ForesterUtil;
18 public class msa_compactor {
20 final static private String HELP_OPTION_1 = "help";
21 final static private String HELP_OPTION_2 = "h";
22 final static private String REMOVE_WORST_OFFENDERS_OPTION = "w";
23 final static private String AV_GAPINESS_OPTION = "a";
24 final static private String STEP_OPTION = "s";
25 final static private String LENGTH_OPTION = "l";
26 final static private String REALIGN_OPTION = "r";
27 final static private String DO_NOT_NORMALIZE_FOR_EFF_LENGTH_OPTION = "nn";
28 final static private String PRG_NAME = "msa_compactor";
29 final static private String PRG_DESC = "multiple sequnce aligment compactor";
30 final static private String PRG_VERSION = "0.01";
31 final static private String PRG_DATE = "140221";
32 final static private String E_MAIL = "phylosoft@gmail.com";
33 final static private String WWW = "https://sites.google.com/site/cmzmasek/home/software/forester";
35 public static void main( final String args[] ) {
37 final CommandLineArguments cla = new CommandLineArguments( args );
38 if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) || ( cla.getNumberOfNames() != 2 ) ) {
42 final File in = cla.getFile( 0 );
43 final File out = cla.getFile( 1 );
44 int worst_remove = -1;
48 boolean realign = false;
50 final List<String> allowed_options = new ArrayList<String>();
51 allowed_options.add( REMOVE_WORST_OFFENDERS_OPTION );
52 allowed_options.add( AV_GAPINESS_OPTION );
53 allowed_options.add( LENGTH_OPTION );
54 allowed_options.add( REALIGN_OPTION );
55 allowed_options.add( DO_NOT_NORMALIZE_FOR_EFF_LENGTH_OPTION );
56 allowed_options.add( STEP_OPTION );
57 final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
58 if ( dissallowed_options.length() > 0 ) {
59 ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );
61 if ( cla.isOptionSet( REMOVE_WORST_OFFENDERS_OPTION ) ) {
62 worst_remove = cla.getOptionValueAsInt( REMOVE_WORST_OFFENDERS_OPTION );
64 if ( cla.isOptionSet( AV_GAPINESS_OPTION ) ) {
65 av = cla.getOptionValueAsDouble( AV_GAPINESS_OPTION );
67 if ( cla.isOptionSet( LENGTH_OPTION ) ) {
68 length = cla.getOptionValueAsInt( LENGTH_OPTION );
70 if ( cla.isOptionSet( STEP_OPTION ) ) {
71 step = cla.getOptionValueAsInt( STEP_OPTION );
73 if ( cla.isOptionSet( REALIGN_OPTION ) ) {
76 if ( cla.isOptionSet( DO_NOT_NORMALIZE_FOR_EFF_LENGTH_OPTION ) ) {
79 // else if ( cla.isOptionSet( STEP_OPTION ) && cla.isOptionSet( WINDOW_OPTION ) ) {
80 // step = cla.getOptionValueAsInt( STEP_OPTION );
81 // window = cla.getOptionValueAsInt( WINDOW_OPTION );
88 final FileInputStream is = new FileInputStream( in );
89 if ( FastaParser.isLikelyFasta( in ) ) {
90 msa = FastaParser.parseMsa( is );
93 msa = GeneralMsaParser.parse( is );
95 MsaCompactor mc = null;
96 if ( worst_remove > 0 ) {
97 mc = MsaCompactor.removeWorstOffenders( msa, worst_remove, realign, norm );
100 mc = MsaCompactor.reduceGapAverage( msa, av, step, realign, out, 50 );
102 else if ( length > 0 ) {
103 mc = MsaCompactor.reduceLength( msa, length, step, realign );
105 System.out.println( MsaMethods.calcGapRatio( mc.getMsa() ) );
106 for( final String id : mc.getRemovedSeqIds() ) {
107 System.out.println( id );
109 mc.writeMsa( out, MSA_FORMAT.PHYLIP, ".aln" );
111 catch ( final Exception e ) {
113 ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
117 private static void printHelp() {
118 ForesterUtil.printProgramInformation( PRG_NAME,
124 ForesterUtil.getForesterLibraryInformation() );
125 System.out.println( "Usage:" );
126 System.out.println();
127 System.out.println( PRG_NAME + " <options> <msa input file>" );
128 System.out.println();
129 System.out.println( " options: " );
130 System.out.println();
131 System.out.println( " -" + REMOVE_WORST_OFFENDERS_OPTION + "=<integer>: step size (msa columns)" );
132 System.out.println();
133 System.out.println();
134 System.out.println();