Loading data
From Jstacs
Most simple way for loading DNA-sequences from a FastA file:
Sample data = new DNASample( home+"myfile.fa" );
Loading DNA-sequences from a FastA file:
//create a DNA-alphabet AlphabetContainer container = new AlphabetContainer( new DNAAlphabet() ); //create a Sample using the alphabet from above in FastA-format data = new Sample( container, new SparseStringExtractor( home+"myfile.fa", StringExtractor.FASTA ));
Loading DNA-sequences from a plain text file:
//create a DNA-alphabet AlphabetContainer container = new AlphabetContainer( new DNAAlphabet() ); //create a Sample using the alphabet from above data = new Sample( container, new SparseStringExtractor( home+"myfile.txt" ));
Creating a Sample from a BioJava SequenceIterator:
//defining the ids, we want to obtain from NCBI Genbank: GenbankRichSequenceDB db = new GenbankRichSequenceDB(); SimpleSequenceIterator it = new SimpleSequenceIterator( db.getRichSequence( "NC_001284.2" ), db.getRichSequence( "NC_000932.1" ) ); //conversion to Jstacs Sample Sample data = BioJavaAdapter.sequenceIteratorToSample( it, null );
