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andreasprlicandreasprlic
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adding a couple of demo files to the core project
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‎biojava-core/src/main/java/demo/DemoSixFrameTranslation.java‎

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package demo;
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import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
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import org.biojava.nbio.core.sequence.DNASequence;
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import org.biojava.nbio.core.sequence.ProteinSequence;
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import org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundSet;
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import org.biojava.nbio.core.sequence.compound.AmbiguityRNACompoundSet;
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import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
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import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
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import org.biojava.nbio.core.sequence.io.DNASequenceCreator;
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import org.biojava.nbio.core.sequence.io.FastaReader;
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import org.biojava.nbio.core.sequence.io.GenericFastaHeaderParser;
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import org.biojava.nbio.core.sequence.template.CompoundSet;
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import org.biojava.nbio.core.sequence.template.Sequence;
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import org.biojava.nbio.core.sequence.transcription.Frame;
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import org.biojava.nbio.core.sequence.transcription.TranscriptionEngine;
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import java.io.ByteArrayInputStream;
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import java.io.InputStream;
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import java.util.LinkedHashMap;
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import java.util.Map;
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/**
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* Created by andreas on 8/10/15.
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*/
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public class DemoSixFrameTranslation {
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public static void main(String[] args){
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String dnaFastaS = ">gb:GQ903697|Organism:Arenavirus H0030026 H0030026|Segment:S|Host:Rat\n" +
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"CGCACAGAGGATCCTAGGCGTTACTGACTTGCGCTAATAACAGATACTGTTTCATATTTAGATAAAGACC\n" +
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"CAGCCAACTGATTGGTCAGCATGGGACAACTTGTGTCCCTCTTCAGTGAAATTCCATCAATCATACACGA\n" +
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"AGCTCTCAATGTTGCTCTCGTAGCTGTTAGCATCATTGCAATATTGAAAGGGGTTGTGAATGTTTGGAAG\n" +
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"AGTGGAGTTTTGCAGCTTTTGGCCTTCTTGCTCCTGGCGGGAAGATCCTGCTCAGTCATAATTGGTCATC\n" +
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"ATCTCGAACTGCAGCATGTGATCTTCAATGGGTCATCAATCACACCCTTTTTACCAGTTACATGTAAGAT\n" +
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"CAATGATACCTACTTCCTACTAAGAGGCCCCTATGAAGCTGATTGGGCAGTTGAATTGAGTGTAACTGAA\n" +
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"ACCACAGTCTTGGTTGATCTTGAAGGTGGCAGCTCAATGAAGCTGAAAGCCGGAAACATCTCAGGTTGTC\n" +
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"TTGGAGACAACCCCCATCTGAGATCAGTGGTCTTCACATTGAATTGGTTGCTAACAGGATTAGATCATGT\n" +
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"TATTGATTCTGACCCGAAAATTCTCTGTGATCTTAAAGACAGTGGGCACTTTCGTCTCCAGATGAACTTA\n" +
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"ACAGAAAAGCACTATTGTGACAAGTTTCACATCAAAATGGGCAAGGTCTTTGGCGTATTCAAAGATCCGT\n" +
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"GCATGGCTGGTGGTAAAATGTTTGCCATACTAAAAAATACCTCTTGGTCGAACCAGTGCCAAGGAAACCA\n" +
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"TGTCAGCACCATTCATCTTGTCCTTCAGAGTAATTTCAAACAGGTCCTCAGTAGCAGGAAACTGTTGAAC\n" +
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"TTTTTCAGCTGGTCATTGTCTGATGCCACAGGGGCTGATATGCCTGGTGGTTTTTGTCTGGAAAAATGGA\n" +
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"TGTTGATTTCAAGTGAACTGAAATGCTTTGGAAACACAGCTGTGGCAAAGTGCAACTTAAATCATGACTC\n" +
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"AGAGTTCTGTGACATGCTTAGGCTTTTTGATTTCAACAAAAAGGCAATAGTCACTCTTCAGAACAAAACA\n" +
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"AAGCATCGGCTGGACACAGTAATTACTGCTATCAATTCATTGATCTCTGATAATATTCTTATGAAGAACA\n" +
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"GGATTAAAGAATTGATAGATGTTCCTTACTGTAATTACACCAAATTTTGGTATGTCAATCACACAGGTCT\n" +
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"AAATCTGCACACCCTTCCAAGATGTTGGCTTGTTAAAAATGGTAGCTACTTGAATGTGTCTGACTTCAGG\n" +
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"AATGAGTGGATATTGGAGAGTGATCATCTTGTTTCGGAGATCCTTTCAAAGGAGTATGAGGAAAGGCAAA\n" +
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"ATCGTACACCACTCTCACTGGTTGACATCTGTTTCTGGAGTACATTGTTTTACACAGCATCAATTTTCCT\n" +
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"ACACCTCTTGAGAATTCCAACCCACAGACACATTGTTGGTGAGGGCTGCCCGAAGCCTCATAGGCTAAAC\n" +
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"AGGCACTCAATATGTGCTTGTGGCCTTTTCAAACAAGAAGGCAGACCCTTGAGATGGGTAAGAAAGGTGT\n" +
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"GAACAATGGTTGCTTGGTGGCCTCCATTGCTGCACCCCCCTAGGGGGGTGCAGCAATGGAGGTTCTCGYT\n" +
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"GAGCCTAGAGAACAACTGTTGAATCGGGTTCTCTAAAGAGAACATCGATTGGTAGTACCCTTTTTGGTTT\n" +
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"TTCATTGGTCACTGACCCTGAAAGCACAGCACTGAACATCAAACAGTCCAAAAGTGCACAGTGTGCATTT\n" +
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"GTTGTGGCTGGTGCTGATCCTTTCTTCTTACTTTTAATGACTATTCCCTTATGTCTGTCACACAGATGTT\n" +
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"CAAATCTCTTCCAAACAAGATCTTCAAAGAGCCGTGACTGTTCTGCGGTCAGTTTGACATCAACAATCTT\n" +
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"CAAATCCTGTCTTCCATGCATATCAAAGAGCCTCCTAATATCATCAGCACCTTGCGCAGTGAAAACCATG\n" +
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"GATTTAGGCAGACTCCTTATTATGCTTGTGATGAGGCCAGGTCGTGCATGTTCAACATCCTTCAGCAATA\n" +
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"TCCCATGACAATATTTACTTTGGTCCTTAAAAGATTTTATGTCATTGGGTTTTCTGTAGCAGTGGATGAA\n" +
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"TTTTTGTGATTCAGGCTGGTAAATTGCAAACTCAACAGGGTCATGTGGCGGGCCTTCAATGTCAATCCAT\n" +
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"GTTGTGTCACTGACCATCAACGACTCTACACTTCTCTTCACCTGAGCCTCCACCTCAGGCTTGAGCGTGG\n" +
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"ACAAGAGTGGGGCACCACCGTTCCGGATGGGGACTGGTGTTTTGCTTGGTAAACTCTCAAATTCCACAAC\n" +
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"TGTATTGTCCCATGCTCTCCCTTTGATCTGTGATCTTGATGAAATGTAAGGCCAGCCCTCACCAGAGAGA\n" +
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"CACACCTTATAAAGTATGTTTTCATAAGGATTCCTCTGTCCTGGTATGGCACTGATGAACATGTTTTCCC\n" +
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"TCTTTTTGATCTCCAAGAGGGTTTTTATAATGGTTGTGAATGTGGACTCCTCAATCTTTATTGTTTCCAG\n" +
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"CATGTTGCCACCATCAATCAGGCAAGCACCGGCTTTCACAGCAGCTGATAAACTAAGGTTGTAGCCTGAT\n" +
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"ATGTTAATTTGAGAATCCTCCTGAGTGATTACCTTTAGAGAAGGATGCTTCTCCATCAAAGCATCTAAGT\n" +
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"CACTTAAATTAGGGTATTTTGCTGTGTATAGCAACCCCAGATCTGTGAGGGCCTGAACCACATCATTTAG\n" +
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"AGTTTCCCCTCCCTGTTCAGTCATACAGGAAATTGTGAGTGCTGGCATCGATCCAAATTGGTTGATCATA\n" +
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"AGTGATGAGTCTTTAACGTCCCAGACTTTGACCACCCCTCCAGTTCTAGCCAACCCAGGTCTCTGAATAC\n" +
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"CAACAAGTTGCAGAATTTCGGACCTCCTGGTGAGCTGTGTTGTAGAGAGGTTCCCTAGATACTGGCCACC\n" +
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"TGTGGCTGTCAACCTCTCTGTTCTTTGAACTTTTTGCCTTAATTTGTCCAAGTCACTGGAGAGTTCCATT\n" +
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"AGCTCTTCCTTTGACAATGATCCTATCTTAAGGAACATGTTCTTTTGGGTTGACTTCATGACCATCAATG\n" +
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"AGTCAACTTCCTTATTCAAGTCCCTCAAACTAACAAGATCACTGTCATCTCTTTTAGACCTCCTCATCAT\n" +
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"GCGTTGCACACTTGCAACCTTTGAAAAATCTAAGCCGGACAGAAGAGCCCTCGCGTCAGTTAGGACATCT\n" +
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"GCCTTAACAGCAGTTGTCCAGTTCGAGAGTCCTCTCCTGAGAGACTGTGTCCATCTGAATGATGGGATTG\n" +
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"GTTGTTCGCTCATAGTGATGAAATTGCGCAGAGTTATCCAAAAGCCTAGGATCCTCTGTGCG";
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try {
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// parse the raw sequence from the string
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InputStream stream = new ByteArrayInputStream(dnaFastaS.getBytes());
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// define the Ambiguity Compound Sets
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AmbiguityDNACompoundSet ambiguityDNACompoundSet = AmbiguityDNACompoundSet.getDNACompoundSet();
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CompoundSet<NucleotideCompound> nucleotideCompoundSet = AmbiguityRNACompoundSet.getRNACompoundSet();
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FastaReader<DNASequence, NucleotideCompound> proxy =
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new FastaReader<DNASequence, NucleotideCompound>(
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stream,
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new GenericFastaHeaderParser<DNASequence, NucleotideCompound>(),
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new DNASequenceCreator(ambiguityDNACompoundSet));
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// has only one entry in this example, but could be easily extended to parse a FASTA file with multiple sequences
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LinkedHashMap<String, DNASequence> dnaSequences = proxy.process();
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// Initialize the Transcription Engine
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TranscriptionEngine engine = new
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TranscriptionEngine.Builder().dnaCompounds(ambiguityDNACompoundSet).rnaCompounds(nucleotideCompoundSet).build();
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Frame[] sixFrames = Frame.getAllFrames();
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for (DNASequence dna : dnaSequences.values()) {
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Map<Frame, Sequence<AminoAcidCompound>> results = engine.multipleFrameTranslation(dna, sixFrames);
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for (Frame frame : sixFrames){
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System.out.println("Translated Frame:" + frame +" : " + results.get(frame));
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//System.out.println(dna.getRNASequence(frame).getProteinSequence(engine));
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ProteinSequence ps = new ProteinSequence(results.get(frame).getSequenceAsString());
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System.out.println(ps);
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try {
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} catch (Exception e){
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System.err.println(e.getMessage() + " when trying to translate frame " + frame);
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}
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}
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}
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} catch (Exception e){
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e.printStackTrace();
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}
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}
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}

‎biojava-core/src/main/java/demo/ParseFastaFileDemo.java‎

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package demo;
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import java.io.File;
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import java.io.FileInputStream;
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import java.io.IOException;
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import java.io.InputStream;
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import java.util.LinkedHashMap;
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import java.util.logging.Level;
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import java.util.logging.Logger;
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import org.biojava.nbio.core.sequence.ProteinSequence;
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import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
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import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
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import org.biojava.nbio.core.sequence.io.FastaReader;
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import org.biojava.nbio.core.sequence.io.GenericFastaHeaderParser;
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import org.biojava.nbio.core.sequence.io.ProteinSequenceCreator;
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import org.biojava.nbio.core.util.InputStreamProvider;
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/**
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* Created by andreas on 6/17/15.
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*/
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public class ParseFastaFileDemo {
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public ParseFastaFileDemo(){
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}
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/** e.g. download ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz
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* and pass in path to local location of file
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*
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* @param args
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*/
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public static void main(String[] args) {
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int mb = 1024*1024;
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//Getting the runtime reference from system
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Runtime runtime = Runtime.getRuntime();
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System.out.println("##### Heap utilization statistics [MB] #####");
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//Print used memory
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System.out.println("Used Memory:"
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+ (runtime.totalMemory() - runtime.freeMemory()) / mb);
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//Print free memory
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System.out.println("Free Memory:"
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+ runtime.freeMemory() / mb);
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//Print total available memory
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System.out.println("Total Memory:" + runtime.totalMemory() / mb);
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//Print Maximum available memory
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System.out.println("Max Memory:" + runtime.maxMemory() / mb);
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if ( args.length < 1) {
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System.err.println("First argument needs to be path to fasta file");
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return;
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}
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File f = new File(args[0]);
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if ( ! f.exists()) {
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System.err.println("File does not exist " + args[0]);
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return;
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}
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long timeS = System.currentTimeMillis();
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try {
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// automatically uncompress files using InputStreamProvider
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InputStreamProvider isp = new InputStreamProvider();
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InputStream inStream = isp.getInputStream(f);
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FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<ProteinSequence, AminoAcidCompound>(
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inStream,
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new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(),
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new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
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LinkedHashMap<String, ProteinSequence> b;
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int nrSeq = 0;
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while ((b = fastaReader.process(100)) != null) {
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for (String key : b.keySet()) {
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nrSeq++;
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//System.out.println(nrSeq + " : " + key + " " + b.get(key));
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if ( nrSeq % 100000 == 0)
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System.out.println(nrSeq );
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}
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}
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long timeE = System.currentTimeMillis();
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System.out.println("parsed a total of " + nrSeq + " TREMBL sequences! in " + (timeE - timeS));
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} catch (Exception ex) {
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Logger.getLogger(ParseFastaFileDemo.class.getName()).log(Level.SEVERE, null, ex);
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}
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}
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}

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