//
//
// "java -Xmx1024m -cp path\to\forester.jar org.forester.application.fasta_split
-//
+//
//
package org.forester.application;
final static private String PRG_NAME = "fasta_split";
final static private String PRG_VERSION = "1.00";
- final static private String PRG_DATE = "150325";
+ final static private String PRG_DATE = "150331";
public static void main( final String args[] ) {
ForesterUtil.printProgramInformation( fasta_split.PRG_NAME, fasta_split.PRG_VERSION, fasta_split.PRG_DATE );
if ( !ForesterUtil.isEmpty( error ) ) {
ForesterUtil.fatalError( PRG_NAME, error );
}
+ if ( !outdir.exists() ) {
+ new File( outdir.toString() ).mkdir();
+ }
if ( !outdir.isDirectory() ) {
ForesterUtil.fatalError( PRG_NAME, outdir + " is not a directory" );
}
if ( ( seqs == null ) || seqs.isEmpty() ) {
ForesterUtil.fatalError( PRG_NAME, infile + " appears empty" );
}
+ System.out.println( "Read " + seqs.size() + " sequences" );
final Map<String, List<MolecularSequence>> output = new HashMap<String, List<MolecularSequence>>();
int cc = 0;
for( final MolecularSequence seq : seqs ) {
- System.out.println( ++cc );
+ ++cc;
final Matcher m = pa.matcher( seq.getIdentifier() );
if ( m.find() ) {
final String key = m.group( 1 );
output.get( key ).add( seq );
}
else {
- //ForesterUtil.fatalError( PRG_NAME, pattern_str + " not found in sequence \"" + seq.getIdentifier() + "\"" );
- System.out.println( "warning: " + pattern_str + " not found in sequence \"" + seq.getIdentifier() + "\"" );
+ System.out.println( "warning: " + pattern_str + " not found in sequence \"" + seq.getIdentifier()
+ + "\"" );
final String key = "unknown";
if ( !output.containsKey( key ) ) {
output.put( key, new ArrayList<MolecularSequence>() );
}
int c = 0;
for( final Map.Entry<String, List<MolecularSequence>> entry : output.entrySet() ) {
- final File of = new File( outdir.getAbsolutePath().toString() + "/" + entry.getKey() + ".fasta" );
+ String s = entry.getKey();
+ s = s.replace( '*', '_' );
+ final File of = new File( outdir.getAbsolutePath().toString() + "/" + s + ".fasta" );
if ( of.exists() ) {
ForesterUtil.fatalError( PRG_NAME, of + " already exists" );
}
- System.out.println( ++c + ": writing " + of );
+ System.out.println( ++c + ": writing " + of + " [" + entry.getValue().size() + " seqs]" );
try {
SequenceWriter.writeSeqs( entry.getValue(), of, SEQ_FORMAT.FASTA, 60 );
}
private static void argumentsError() {
System.out.println( PRG_NAME + " <pattern> <infile> <outdir>" );
+ System.out.println( "Example: " + PRG_NAME + " \"v-germ=(\\S+)\" tt.fasta outdir" );
System.out.println();
System.exit( -1 );
}