public static void main(String[] args) {
try {
ArrayList<GeneSequence> sequences = new ArrayList<GeneSequence>();
ChromosomeSequence seq1 =
new ChromosomeSequence(
"ATATATATATATATATATATATATATATATATACGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCATATATATATATATATATATATACGCGCGCGCGCGCGCGCATATATATATATATATATATATATATATATATACGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCATATATATATATATATATATATACGCGCGCGCGCGCGCGC");
GeneSequence gene1 = seq1.addGene(new AccessionID("gene1"), 1, 20, Strand.POSITIVE);
gene1.addExon(new AccessionID("t1_1_10"), 1, 10);
gene1.addExon(new AccessionID("t1_12_15"), 12, 15);
GeneSequence gene2 = seq1.addGene(new AccessionID("gene2"), 1, 20, Strand.NEGATIVE);
gene2.addExon(new AccessionID("t2_1_10"), 1, 10);
gene2.addExon(new AccessionID("t2_12_15"), 12, 15);
sequences.add(gene1);
sequences.add(gene2);
FastaGeneWriter fastaWriter =
new FastaGeneWriter(
System.out,
sequences,
new GenericFastaHeaderFormat<GeneSequence, NucleotideCompound>(),
true);
fastaWriter.process();
} catch (Exception e) {
e.printStackTrace();
}
}
