From: cmzmasek Date: Wed, 30 Aug 2017 17:49:33 +0000 (-0700) Subject: in progress... X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=6e2f7ce504c31ed655f08dfbadbed98e084853b9 in progress... --- diff --git a/forester/java/src/org/forester/application/tap.java b/forester/java/src/org/forester/application/tap.java new file mode 100644 index 0000000..2fcf2cc --- /dev/null +++ b/forester/java/src/org/forester/application/tap.java @@ -0,0 +1,211 @@ + +package org.forester.application; + +import java.io.BufferedWriter; +import java.io.File; +import java.io.FileInputStream; +import java.io.IOException; +import java.io.Writer; +import java.util.ArrayList; +import java.util.List; + +import org.forester.io.parsers.FastaParser; +import org.forester.io.parsers.GeneralMsaParser; +import org.forester.io.writers.SequenceWriter; +import org.forester.io.writers.SequenceWriter.SEQ_FORMAT; +import org.forester.msa.BasicMsa; +import org.forester.msa.Msa; +import org.forester.msa.Msa.MSA_FORMAT; +import org.forester.sequence.BasicSequence; +import org.forester.sequence.MolecularSequence; +import org.forester.util.CommandLineArguments; +import org.forester.util.ForesterConstants; +import org.forester.util.ForesterUtil; + +public class tap { + + final static private String PRG_NAME = "tap"; + final static private String PRG_DATE = "170327"; + final static private String PRG_DESC = "Replacement of labels in multiple sequence files"; + final static private String PRG_VERSION = "1.00"; + final static private String WWW = "https://sites.google.com/site/cmzmasek/home/software/forester"; + final static private String E_MAIL = "phyloxml@gmail.com"; + final static private String EXTRACT_TAXONOMY_OPTION = "t"; + final static private String ANNOTATION_OPTION = "a"; + final static private String HELP_OPTION_1 = "help"; + final static private String HELP_OPTION_2 = "h"; + + public static void main( final String args[] ) { + try { + ForesterUtil.printProgramInformation( PRG_NAME, + PRG_DESC, + PRG_VERSION, + PRG_DATE, + E_MAIL, + WWW, + ForesterUtil.getForesterLibraryInformation() ); + CommandLineArguments cla = null; + try { + cla = new CommandLineArguments( args ); + } + catch ( final Exception e ) { + ForesterUtil.fatalError( PRG_NAME, e.getMessage() ); + } + if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) ) { + System.out.println(); + print_help(); + System.exit( 0 ); + } + String input = null; + String output = null; + String list_file = null; + String i = null; + if ( args.length == 3 ) { + input = cla.getName( 0 ); + output = cla.getName( 1 ); + list_file = cla.getName( 2 ); + } + else if ( args.length == 1 ) { + input = cla.getName( 0 ); + i = null; + if ( input.toLowerCase().endsWith( ".fasta" ) ) { + i = input.substring( 0, input.length() - 7 ); + } + else if ( input.toLowerCase().endsWith( ".fsa" ) ) { + i = input.substring( 0, input.length() - 5 ); + } + else { + i = input; + } + output = i + ForesterConstants.ID_NORMALIZED_FASTA_FILE_SUFFIX; + list_file = i + ForesterConstants.ID_MAP_FILE_SUFFIX; + } + else { + print_help(); + System.exit( -1 ); + } + final List allowed_options = new ArrayList<>(); + allowed_options.add( ANNOTATION_OPTION ); + final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options ); + if ( dissallowed_options.length() > 0 ) { + ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options ); + } + final File outfile_file = new File( output ); + final File listfile = new File( list_file ); + final File input_file = new File( input ); + final String error1 = ForesterUtil.isWritableFile( outfile_file ); + if ( !ForesterUtil.isEmpty( error1 ) ) { + ForesterUtil.fatalError( PRG_NAME, error1 ); + } + final String error2 = ForesterUtil.isWritableFile( listfile ); + if ( !ForesterUtil.isEmpty( error2 ) ) { + ForesterUtil.fatalError( PRG_NAME, error2 ); + } + final String error3 = ForesterUtil.isReadableFile( input_file ); + if ( !ForesterUtil.isEmpty( error3 ) ) { + ForesterUtil.fatalError( PRG_NAME, error3 ); + } + final boolean fasta_like = ForesterUtil.isLooksLikeFasta( input_file ); + final Msa.MSA_FORMAT output_format = MSA_FORMAT.FASTA; + System.out.println(); + System.out.println( "Input alignment : " + input ); + System.out.println( "Output alignment : " + output ); + System.out.println( "Name list : " + list_file ); + if ( fasta_like ) { + System.out.println( "Input format : Fasta" ); + } + else { + System.out.println( "Input format : Phylip like" ); + } + if ( output_format == MSA_FORMAT.FASTA ) { + System.out.println( "Output format : Fasta" ); + } + else if ( output_format == MSA_FORMAT.NEXUS ) { + System.out.println( "Output format : Nexus" ); + } + else if ( output_format == MSA_FORMAT.PHYLIP ) { + System.out.println( "Output format : Phylip" ); + } + System.out.println(); + + final List seqs; + final FileInputStream is = new FileInputStream( input_file ); + if ( FastaParser.isLikelyFasta( input_file ) ) { + seqs = FastaParser.parse( is ); + } + else { + seqs = GeneralMsaParser.parseSeqs( is ); + } + if ( seqs == null ) { + ForesterUtil.fatalError( PRG_NAME, "failed to read MSA" ); + } + if ( seqs.size() < 1 ) { + ForesterUtil.fatalError( PRG_NAME, "MSA seems to be devoid of sequences" ); + } + // TODO print number of seqs + // TODO print number min length + // TODO print max length + // TODO OR + // TODO print length is aligned + // TODO if no aligned no phylip or nexus outpt + // + + final List seqs2 = new ArrayList<>(); + int counter = 0; + final BufferedWriter writer = ForesterUtil.createBufferedWriter( list_file ); + for( final MolecularSequence seq : seqs ) { + final String new_name = modify_name( seq.getIdentifier(), counter++, writer ); + final MolecularSequence ns = BasicSequence.createSequence( new_name, + seq.getMolecularSequenceAsString() ); + seqs2.add( ns ); + } + writer.flush(); + writer.close(); + final BufferedWriter seq_writer = ForesterUtil.createBufferedWriter( outfile_file ); + if ( ( output_format == MSA_FORMAT.NEXUS ) || ( output_format == MSA_FORMAT.PHYLIP ) ) { + final Msa m = BasicMsa.createInstance( seqs2 ); + m.write( seq_writer, output_format ); + } + else if ( output_format == MSA_FORMAT.FASTA ) { + SequenceWriter.writeSeqs( seqs2, seq_writer, SEQ_FORMAT.FASTA, 60 ); + } + seq_writer.flush(); + seq_writer.close(); + // Util.print_message( PRG_NAME, "wrote: " + list_file ) + // Util.print_message( PRG_NAME, "wrote: " + output ) + } + catch ( final IllegalArgumentException e ) { + ForesterUtil.fatalError( PRG_NAME, e.getMessage() ); + } + catch ( final Exception e ) { + e.printStackTrace(); + ForesterUtil.fatalError( PRG_NAME, "Unexpected errror!" ); + } + } + + final static String modify_name( final String desc, final int counter, final Writer writer ) throws IOException { + desc.replaceAll( "\\s+", " " ); + final String new_desc = Integer.toHexString( counter ); + if ( new_desc.length() > 9 ) { + ForesterUtil.fatalError( PRG_NAME, + "shortened identifier [" + new_desc + "] is too long (" + new_desc.length() + + " characters)" ); + } + writer.write( new_desc + "\t" + desc + "\n" ); + return new_desc; + } + + private final static void print_help() { + System.out.println( "Usage:" ); + System.out.println(); + System.out.println( PRG_NAME + " [options] " ); + System.out.println(); + System.out.println( " options:" ); + //System.out.println( " -" + SEP_OPTION + "=: the separator to be used" ); + System.out.println(); + System.out.println( "Example:" ); + System.out.println(); + System.out.println( " " + PRG_NAME + " -s=. my_tree.xml A.1.1.1" ); + System.out.println(); + } +}