import org.forester.util.DescriptiveStatistics;
import org.forester.util.ForesterUtil;
+
+/*
+java -cp C:\Users\czmasek\SOFTWARE_DEV\ECLIPSE\forester\java\fo
+rester.jar org.forester.application.msa_compactor Bcl-2_e1_20_mafft -t
+*/
+
public class msa_compactor {
final private static NumberFormat NF_1 = new DecimalFormat( "0.#" );
final static private String STEP_OPTION = "s";
final static private String LENGTH_OPTION = "l";
final static private String REALIGN_OPTION = "a";
+ final static private String INFO_ONLY_OPTION = "i";
//
final static private String STEP_FOR_DIAGNOSTICS_OPTION = "sd";
final static private String MIN_LENGTH_OPTION = "ml";
allowed_options.add( OUTPUT_REMOVED_SEQS_OPTION );
allowed_options.add( MAFFT_OPTIONS );
allowed_options.add( PERFORM_PHYLOGENETIC_INFERENCE );
+ allowed_options.add( INFO_ONLY_OPTION );
final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
if ( dissallowed_options.length() > 0 ) {
ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );
msa = DeleteableMsa.createInstance( GeneralMsaParser.parse( is ) );
}
final DescriptiveStatistics initial_msa_stats = MsaMethods.calculateEffectiveLengthStatistics( msa );
+ if (cla.isOptionSet( INFO_ONLY_OPTION ) ) {
+ printInfo( in, msa, initial_msa_stats );
+ System.exit( 0 );
+ }
+
final boolean chart_only = ( !cla.isOptionSet( LENGTH_OPTION ) )
&& ( !cla.isOptionSet( REMOVE_WORST_OFFENDERS_OPTION ) )
&& ( !cla.isOptionSet( AV_GAPINESS_OPTION ) && ( !cla.isOptionSet( MIN_LENGTH_OPTION ) ) );
"step for diagnostics reports needs to be set to 1 for tree calculation" );
}
}
- ForesterUtil.printProgramInformation( PRG_NAME,
- PRG_DESC,
- PRG_VERSION,
- PRG_DATE,
- E_MAIL,
- WWW,
- ForesterUtil.getForesterLibraryInformation() );
- System.out.println( "Input MSA : " + in );
- System.out.println( " MSA length : " + msa.getLength() );
- System.out.println( " Number of sequences : " + msa.getNumberOfSequences() );
- System.out.println( " Median sequence length : " + NF_1.format( initial_msa_stats.median() ) );
- System.out.println( " Mean sequence length : "
- + NF_1.format( initial_msa_stats.arithmeticMean() ) );
- System.out.println( " Max sequence length : " + ( ( int ) initial_msa_stats.getMax() ) );
- System.out.println( " Min sequence length : " + ( ( int ) initial_msa_stats.getMin() ) );
- System.out.println( " Gap ratio : "
- + NF_4.format( MsaMethods.calcGapRatio( msa ) ) );
- System.out.println( " Normalized Shannon Entropy (entn21): "
- + NF_4.format( MsaMethods.calcNormalizedShannonsEntropy( 21, msa ) ) );
+ printInfo( in, msa, initial_msa_stats );
if ( !chart_only ) {
System.out.println( "Output : " + out );
}
- else {
- System.out.println( "Output : n/a" );
- }
+
if ( removed_seqs_out_base != null ) {
System.out.println( "Write removed sequences to : " + removed_seqs_out_base );
}
}
}
+ private static void printInfo( final File in, DeleteableMsa msa, final DescriptiveStatistics initial_msa_stats ) {
+ ForesterUtil.printProgramInformation( PRG_NAME,
+ PRG_DESC,
+ PRG_VERSION,
+ PRG_DATE,
+ E_MAIL,
+ WWW,
+ ForesterUtil.getForesterLibraryInformation() );
+ System.out.println( "Input MSA : " + in );
+ System.out.println( " MSA length : " + msa.getLength() );
+ System.out.println( " Number of sequences : " + msa.getNumberOfSequences() );
+ System.out.println( " Median sequence length : " + NF_1.format( initial_msa_stats.median() ) );
+ System.out.println( " Mean sequence length : "
+ + NF_1.format( initial_msa_stats.arithmeticMean() ) );
+ System.out.println( " Max sequence length : " + ( ( int ) initial_msa_stats.getMax() ) );
+ System.out.println( " Min sequence length : " + ( ( int ) initial_msa_stats.getMin() ) );
+ System.out.println( " Gap ratio : "
+ + NF_4.format( MsaMethods.calcGapRatio( msa ) ) );
+ System.out.println( " Mean gap count per 100 residues : "
+ + NF_1.format( MsaMethods.calcNumberOfGapsPer100Stats( msa ).arithmeticMean() ) );
+ System.out.println( " Normalized Shannon Entropy (entn7) : "
+ + NF_4.format( MsaMethods.calcNormalizedShannonsEntropy( 7, msa ) ) );
+ System.out.println( " Normalized Shannon Entropy (entn21): "
+ + NF_4.format( MsaMethods.calcNormalizedShannonsEntropy( 21, msa ) ) );
+ }
+
private static void checkPathToMafft( final String path_to_mafft ) {
if ( !ForesterUtil.isEmpty( path_to_mafft ) && MsaInferrer.isInstalled( path_to_mafft ) ) {
}
}
System.out.println( "Usage:" );
System.out.println();
- System.out.println( PRG_NAME + " <options> <msa input file> <output file base>" );
+ System.out.println( PRG_NAME + " [options] <msa input file> [output file base]" );
System.out.println();
System.out.println( " options: " );
System.out.println();
+ System.out.println( " -" + INFO_ONLY_OPTION
+ + " to only display same basic information about the MSA" );
System.out.println( " -" + REMOVE_WORST_OFFENDERS_OPTION
+ "=<integer> number of worst offender sequences to remove" );
System.out.println( " -" + LENGTH_OPTION + "=<integer> target MSA length" );