/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package demo;
import org.biojava.nbio.core.sequence.DNASequence;
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundSet;
import org.biojava.nbio.core.sequence.compound.AmbiguityRNACompoundSet;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
import org.biojava.nbio.core.sequence.io.DNASequenceCreator;
import org.biojava.nbio.core.sequence.io.FastaReader;
import org.biojava.nbio.core.sequence.io.GenericFastaHeaderParser;
import org.biojava.nbio.core.sequence.template.CompoundSet;
import org.biojava.nbio.core.sequence.template.Sequence;
import org.biojava.nbio.core.sequence.transcription.Frame;
import org.biojava.nbio.core.sequence.transcription.TranscriptionEngine;
import java.io.ByteArrayInputStream;
import java.io.InputStream;
import java.util.LinkedHashMap;
import java.util.Map;
/**
* Created by andreas on 8/10/15.
*/
public class DemoSixFrameTranslation {
public static void main(String[] args){
String dnaFastaS = ">gb:GQ903697|Organism:Arenavirus H0030026 H0030026|Segment:S|Host:Rat\n" +
"CGCACAGAGGATCCTAGGCGTTACTGACTTGCGCTAATAACAGATACTGTTTCATATTTAGATAAAGACC\n" +
"CAGCCAACTGATTGGTCAGCATGGGACAACTTGTGTCCCTCTTCAGTGAAATTCCATCAATCATACACGA\n" +
"AGCTCTCAATGTTGCTCTCGTAGCTGTTAGCATCATTGCAATATTGAAAGGGGTTGTGAATGTTTGGAAG\n" +
"AGTGGAGTTTTGCAGCTTTTGGCCTTCTTGCTCCTGGCGGGAAGATCCTGCTCAGTCATAATTGGTCATC\n" +
"ATCTCGAACTGCAGCATGTGATCTTCAATGGGTCATCAATCACACCCTTTTTACCAGTTACATGTAAGAT\n" +
"CAATGATACCTACTTCCTACTAAGAGGCCCCTATGAAGCTGATTGGGCAGTTGAATTGAGTGTAACTGAA\n" +
"ACCACAGTCTTGGTTGATCTTGAAGGTGGCAGCTCAATGAAGCTGAAAGCCGGAAACATCTCAGGTTGTC\n" +
"TTGGAGACAACCCCCATCTGAGATCAGTGGTCTTCACATTGAATTGGTTGCTAACAGGATTAGATCATGT\n" +
"TATTGATTCTGACCCGAAAATTCTCTGTGATCTTAAAGACAGTGGGCACTTTCGTCTCCAGATGAACTTA\n" +
"ACAGAAAAGCACTATTGTGACAAGTTTCACATCAAAATGGGCAAGGTCTTTGGCGTATTCAAAGATCCGT\n" +
"GCATGGCTGGTGGTAAAATGTTTGCCATACTAAAAAATACCTCTTGGTCGAACCAGTGCCAAGGAAACCA\n" +
"TGTCAGCACCATTCATCTTGTCCTTCAGAGTAATTTCAAACAGGTCCTCAGTAGCAGGAAACTGTTGAAC\n" +
"TTTTTCAGCTGGTCATTGTCTGATGCCACAGGGGCTGATATGCCTGGTGGTTTTTGTCTGGAAAAATGGA\n" +
"TGTTGATTTCAAGTGAACTGAAATGCTTTGGAAACACAGCTGTGGCAAAGTGCAACTTAAATCATGACTC\n" +
"AGAGTTCTGTGACATGCTTAGGCTTTTTGATTTCAACAAAAAGGCAATAGTCACTCTTCAGAACAAAACA\n" +
"AAGCATCGGCTGGACACAGTAATTACTGCTATCAATTCATTGATCTCTGATAATATTCTTATGAAGAACA\n" +
"GGATTAAAGAATTGATAGATGTTCCTTACTGTAATTACACCAAATTTTGGTATGTCAATCACACAGGTCT\n" +
"AAATCTGCACACCCTTCCAAGATGTTGGCTTGTTAAAAATGGTAGCTACTTGAATGTGTCTGACTTCAGG\n" +
"AATGAGTGGATATTGGAGAGTGATCATCTTGTTTCGGAGATCCTTTCAAAGGAGTATGAGGAAAGGCAAA\n" +
"ATCGTACACCACTCTCACTGGTTGACATCTGTTTCTGGAGTACATTGTTTTACACAGCATCAATTTTCCT\n" +
"ACACCTCTTGAGAATTCCAACCCACAGACACATTGTTGGTGAGGGCTGCCCGAAGCCTCATAGGCTAAAC\n" +
"AGGCACTCAATATGTGCTTGTGGCCTTTTCAAACAAGAAGGCAGACCCTTGAGATGGGTAAGAAAGGTGT\n" +
"GAACAATGGTTGCTTGGTGGCCTCCATTGCTGCACCCCCCTAGGGGGGTGCAGCAATGGAGGTTCTCGYT\n" +
"GAGCCTAGAGAACAACTGTTGAATCGGGTTCTCTAAAGAGAACATCGATTGGTAGTACCCTTTTTGGTTT\n" +
"TTCATTGGTCACTGACCCTGAAAGCACAGCACTGAACATCAAACAGTCCAAAAGTGCACAGTGTGCATTT\n" +
"GTTGTGGCTGGTGCTGATCCTTTCTTCTTACTTTTAATGACTATTCCCTTATGTCTGTCACACAGATGTT\n" +
"CAAATCTCTTCCAAACAAGATCTTCAAAGAGCCGTGACTGTTCTGCGGTCAGTTTGACATCAACAATCTT\n" +
"CAAATCCTGTCTTCCATGCATATCAAAGAGCCTCCTAATATCATCAGCACCTTGCGCAGTGAAAACCATG\n" +
"GATTTAGGCAGACTCCTTATTATGCTTGTGATGAGGCCAGGTCGTGCATGTTCAACATCCTTCAGCAATA\n" +
"TCCCATGACAATATTTACTTTGGTCCTTAAAAGATTTTATGTCATTGGGTTTTCTGTAGCAGTGGATGAA\n" +
"TTTTTGTGATTCAGGCTGGTAAATTGCAAACTCAACAGGGTCATGTGGCGGGCCTTCAATGTCAATCCAT\n" +
"GTTGTGTCACTGACCATCAACGACTCTACACTTCTCTTCACCTGAGCCTCCACCTCAGGCTTGAGCGTGG\n" +
"ACAAGAGTGGGGCACCACCGTTCCGGATGGGGACTGGTGTTTTGCTTGGTAAACTCTCAAATTCCACAAC\n" +
"TGTATTGTCCCATGCTCTCCCTTTGATCTGTGATCTTGATGAAATGTAAGGCCAGCCCTCACCAGAGAGA\n" +
"CACACCTTATAAAGTATGTTTTCATAAGGATTCCTCTGTCCTGGTATGGCACTGATGAACATGTTTTCCC\n" +
"TCTTTTTGATCTCCAAGAGGGTTTTTATAATGGTTGTGAATGTGGACTCCTCAATCTTTATTGTTTCCAG\n" +
"CATGTTGCCACCATCAATCAGGCAAGCACCGGCTTTCACAGCAGCTGATAAACTAAGGTTGTAGCCTGAT\n" +
"ATGTTAATTTGAGAATCCTCCTGAGTGATTACCTTTAGAGAAGGATGCTTCTCCATCAAAGCATCTAAGT\n" +
"CACTTAAATTAGGGTATTTTGCTGTGTATAGCAACCCCAGATCTGTGAGGGCCTGAACCACATCATTTAG\n" +
"AGTTTCCCCTCCCTGTTCAGTCATACAGGAAATTGTGAGTGCTGGCATCGATCCAAATTGGTTGATCATA\n" +
"AGTGATGAGTCTTTAACGTCCCAGACTTTGACCACCCCTCCAGTTCTAGCCAACCCAGGTCTCTGAATAC\n" +
"CAACAAGTTGCAGAATTTCGGACCTCCTGGTGAGCTGTGTTGTAGAGAGGTTCCCTAGATACTGGCCACC\n" +
"TGTGGCTGTCAACCTCTCTGTTCTTTGAACTTTTTGCCTTAATTTGTCCAAGTCACTGGAGAGTTCCATT\n" +
"AGCTCTTCCTTTGACAATGATCCTATCTTAAGGAACATGTTCTTTTGGGTTGACTTCATGACCATCAATG\n" +
"AGTCAACTTCCTTATTCAAGTCCCTCAAACTAACAAGATCACTGTCATCTCTTTTAGACCTCCTCATCAT\n" +
"GCGTTGCACACTTGCAACCTTTGAAAAATCTAAGCCGGACAGAAGAGCCCTCGCGTCAGTTAGGACATCT\n" +
"GCCTTAACAGCAGTTGTCCAGTTCGAGAGTCCTCTCCTGAGAGACTGTGTCCATCTGAATGATGGGATTG\n" +
"GTTGTTCGCTCATAGTGATGAAATTGCGCAGAGTTATCCAAAAGCCTAGGATCCTCTGTGCG";
try {
// parse the raw sequence from the string
InputStream stream = new ByteArrayInputStream(dnaFastaS.getBytes());
// define the Ambiguity Compound Sets
AmbiguityDNACompoundSet ambiguityDNACompoundSet = AmbiguityDNACompoundSet.getDNACompoundSet();
CompoundSet<NucleotideCompound> nucleotideCompoundSet = AmbiguityRNACompoundSet.getRNACompoundSet();
FastaReader<DNASequence, NucleotideCompound> proxy =
new FastaReader<DNASequence, NucleotideCompound>(
stream,
new GenericFastaHeaderParser<DNASequence, NucleotideCompound>(),
new DNASequenceCreator(ambiguityDNACompoundSet));
// has only one entry in this example, but could be easily extended to parse a FASTA file with multiple sequences
LinkedHashMap<String, DNASequence> dnaSequences = proxy.process();
// Initialize the Transcription Engine
TranscriptionEngine engine = new
TranscriptionEngine.Builder().dnaCompounds(ambiguityDNACompoundSet).rnaCompounds(nucleotideCompoundSet).build();
Frame[] sixFrames = Frame.getAllFrames();
for (DNASequence dna : dnaSequences.values()) {
Map<Frame, Sequence<AminoAcidCompound>> results = engine.multipleFrameTranslation(dna, sixFrames);
for (Frame frame : sixFrames){
System.out.println("Translated Frame:" + frame +" : " + results.get(frame));
//System.out.println(dna.getRNASequence(frame).getProteinSequence(engine));
ProteinSequence ps = new ProteinSequence(results.get(frame).getSequenceAsString());
System.out.println(ps);
try {
} catch (Exception e){
System.err.println(e.getMessage() + " when trying to translate frame " + frame);
}
}
}
} catch (Exception e){
e.printStackTrace();
}
}
}