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<h1 id="how-to-create-a-pairwise-sequence-alignment-in-biojava">How to create a Pairwise Sequence Alignment in BioJava</h1>
<h2 id="global-alignment">Global alignment</h2>
<java>
package org.biojava.nbio.alignment;
import java.net.URL;
import
org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
import org.biojava.nbio.alignment.template.SequencePair; import
org.biojava.nbio.alignment.template.SubstitutionMatrix; import
org.biojava.nbio.core.sequence.ProteinSequence; import
org.biojava.nbio.core.sequence.compound.AminoAcidCompound; import
org.biojava.nbio.core.sequence.io.FastaReaderHelper;
public class CookbookAlignPairGlobal {
` public static void main(String[] args) {`
` String[] ids = new String[] {"Q21691", "Q21495", "O48771"};`
` try {`
` alignPairGlobal(ids[0], ids[1]);`
` } catch (Exception e){`
` e.printStackTrace();`
` }`
` }`
` private static void alignPairGlobal(String id1, String id2) throws Exception {`
` ProteinSequence s1 = getSequenceForId(id1), s2 = getSequenceForId(id2);`
` SubstitutionMatrix`<aminoacidcompound>` matrix = new SimpleSubstitutionMatrix`<aminoacidcompound>`();`
` SequencePair`<ProteinSequence, AminoAcidCompound>` pair = Alignments.getPairwiseAlignment(s1, s2,`
` PairwiseSequenceAlignerType.GLOBAL, new SimpleGapPenalty(), matrix);`
` System.out.printf("%n%s vs %s%n%s", pair.getQuery().getAccession(), pair.getTarget().getAccession(), pair);`
` }`
` private static ProteinSequence getSequenceForId(String uniProtId) throws Exception {`
` URL uniprotFasta = new URL(String.format("`[`http://www.uniprot.org/uniprot/%s.fasta`](http://www.uniprot.org/uniprot/%s.fasta)`", uniProtId));`
` ProteinSequence seq = FastaReaderHelper.readFastaProteinSequence(uniprotFasta.openStream()).get(uniProtId);`
` System.out.printf("id : %s %s%n%s%n", uniProtId, seq, seq.getOriginalHeader());`
` return seq;`
` }`
}
Local alignment
---------------
<java>
package org.biojava.nbio.alignment;
import java.net.URL;
import
org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
import org.biojava.nbio.alignment.template.SequencePair; import
org.biojava.nbio.alignment.template.SubstitutionMatrix; import
org.biojava.nbio.core.sequence.ProteinSequence; import
org.biojava.nbio.core.sequence.compound.AminoAcidCompound; import
org.biojava.nbio.core.sequence.io.FastaReaderHelper;
public class CookbookAlignPairLocal {
` public static void main(String[] args) {`
` String[] ids = new String[] {"Q21691", "Q21495", "O48771"};`
` try {`
` alignPairLocal(ids[0], ids[1]);`
` } catch (Exception e){`
` e.printStackTrace();`
` }`
` }`
` private static void alignPairLocal(String id1, String id2) throws Exception {`
` ProteinSequence s1 = getSequenceForId(id1), s2 = getSequenceForId(id2);`
` SubstitutionMatrix`<aminoacidcompound>` matrix = new SimpleSubstitutionMatrix`<aminoacidcompound>`();`
` SequencePair`<ProteinSequence, AminoAcidCompound>` pair = Alignments.getPairwiseAlignment(s1, s2,`
` PairwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(), matrix);`
` System.out.printf("%n%s vs %s%n%s", pair.getQuery().getAccession(), pair.getTarget().getAccession(), pair);`
` }`
` private static ProteinSequence getSequenceForId(String uniProtId) throws Exception {`
` URL uniprotFasta = new URL(String.format("`[`http://www.uniprot.org/uniprot/%s.fasta`](http://www.uniprot.org/uniprot/%s.fasta)`", uniProtId));`
` ProteinSequence seq = FastaReaderHelper.readFastaProteinSequence(uniprotFasta.openStream()).get(uniProtId);`
` System.out.printf("id : %s %s%n%s%n", uniProtId, seq, seq.getOriginalHeader());`
` return seq;`
` }`
}
How to concurrently create a PSA for each pair in a sequence list in BioJava
============================================================================
Global alignments
-----------------
<java>
package org.biojava3.alignment;
import java.net.URL; import java.util.ArrayList; import java.util.List;
import
org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
import org.biojava.nbio.alignment.template.SequencePair; import
org.biojava.nbio.alignment.template.SubstitutionMatrix; import
org.biojava.nbio.core.sequence.ProteinSequence; import
org.biojava.nbio.core.sequence.compound.AminoAcidCompound; import
org.biojava.nbio.core.sequence.io.FastaReaderHelper; import
org.biojava.nbio.core.util.ConcurrencyTools;
public class CookbookAlignAllGlobal {
` public static void main(String[] args) {`
` String[] ids = new String[] {"Q21691", "Q21495", "O48771"};`
` try {`
` alignAllGlobal(ids);`
` } catch (Exception e){`
` e.printStackTrace();`
` }`
` }`
` private static void alignAllGlobal(String[] ids) throws Exception {`
` List`<proteinsequence>` lst = new ArrayList`<proteinsequence>`();`
` for (String id : ids) {`
` lst.add(getSequenceForId(id));`
` }`
` SubstitutionMatrix`<aminoacidcompound>` matrix = new SimpleSubstitutionMatrix`<aminoacidcompound>`();`
` List`<SequencePair<ProteinSequence, AminoAcidCompound>`> alig = Alignments.getAllPairsAlignments(lst,`
` PairwiseSequenceAlignerType.GLOBAL, new SimpleGapPenalty(), matrix);`
` for (SequencePair`<ProteinSequence, AminoAcidCompound>` pair : alig) {`
` System.out.printf("%n%s vs %s%n%s", pair.getQuery().getAccession(), pair.getTarget().getAccession(), pair);`
` }`
` ConcurrencyTools.shutdown();`
` }`
` private static ProteinSequence getSequenceForId(String uniProtId) throws Exception {`
` URL uniprotFasta = new URL(String.format("`[`http://www.uniprot.org/uniprot/%s.fasta`](http://www.uniprot.org/uniprot/%s.fasta)`", uniProtId));`
` ProteinSequence seq = FastaReaderHelper.readFastaProteinSequence(uniprotFasta.openStream()).get(uniProtId);`
` System.out.printf("id : %s %s%n%s%n", uniProtId, seq, seq.getOriginalHeader());`
` return seq;`
` }`
}
Local alignments
----------------
<java>
package org.biojava3.alignment;
import java.net.URL; import java.util.ArrayList; import java.util.List;
import
org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
import org.biojava.nbio.alignment.template.SequencePair; import
org.biojava.nbio.alignment.template.SubstitutionMatrix; import
org.biojava.nbio.core.sequence.ProteinSequence; import
org.biojava.nbio.core.sequence.compound.AminoAcidCompound; import
org.biojava.nbio.core.sequence.io.FastaReaderHelper; import
org.biojava.nbio.core.util.ConcurrencyTools;
public class CookbookAlignAllLocal {
` public static void main(String[] args) {`
` String[] ids = new String[] {"Q21691", "Q21495", "O48771"};`
` try {`
` alignAllLocal(ids);`
` } catch (Exception e){`
` e.printStackTrace();`
` }`
` }`
` private static void alignAllLocal(String[] ids) throws Exception {`
` List`<proteinsequence>` lst = new ArrayList`<proteinsequence>`();`
` for (String id : ids) {`
` lst.add(getSequenceForId(id));`
` }`
` SubstitutionMatrix`<aminoacidcompound>` matrix = new SimpleSubstitutionMatrix`<aminoacidcompound>`();`
` List`<SequencePair<ProteinSequence, AminoAcidCompound>`> alig = Alignments.getAllPairsAlignments(lst,`
` PairwiseSequenceAlignerType.LOCAL, new SimpleGapPenalty(), matrix);`
` for (SequencePair`<ProteinSequence, AminoAcidCompound>` pair : alig) {`
` System.out.printf("%n%s vs %s%n%s", pair.getQuery().getAccession(), pair.getTarget().getAccession(), pair);`
` }`
` ConcurrencyTools.shutdown();`
` }`
` private static ProteinSequence getSequenceForId(String uniProtId) throws Exception {`
` URL uniprotFasta = new URL(String.format("`[`http://www.uniprot.org/uniprot/%s.fasta`](http://www.uniprot.org/uniprot/%s.fasta)`", uniProtId));`
` ProteinSequence seq = FastaReaderHelper.readFastaProteinSequence(uniprotFasta.openStream()).get(uniProtId);`
` System.out.printf("id : %s %s%n%s%n", uniProtId, seq, seq.getOriginalHeader());`
` return seq;`
` }`
}
</aminoacidcompound></aminoacidcompound></proteinsequence></proteinsequence></java></aminoacidcompound></aminoacidcompound></proteinsequence></proteinsequence></java></aminoacidcompound></aminoacidcompound></java></aminoacidcompound></aminoacidcompound></java>