demo.DemoAlignmentFromFasta Maven / Gradle / Ivy
/*
* 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
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*/
package demo;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.UnsupportedEncodingException;
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
import org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreator;
import org.biojava.nbio.core.sequence.io.GenericFastaHeaderParser;
import org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface;
import org.biojava.nbio.core.sequence.io.template.SequenceHeaderParserInterface;
import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.ResidueNumber;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.StructureTools;
import org.biojava.nbio.structure.align.gui.StructureAlignmentDisplay;
import org.biojava.nbio.structure.align.model.AFPChain;
import org.biojava.nbio.structure.align.util.AlignmentTools;
import org.biojava.nbio.structure.align.util.AtomCache;
import org.biojava.nbio.structure.io.FastaStructureParser;
import org.biojava.nbio.structure.io.StructureSequenceMatcher;
/**
* Demo of how to use the {@link FastaStructureParser} class to read protein
* structures from a FASTA file.
*
* @author Spencer Bliven
*
*/
public class DemoAlignmentFromFasta {
public static void getAlignmentFromFasta() throws StructureException {
// Load a test sequence
// Normally this would come from a file, eg
// File fasta = new File("/path/to/file.fa");
String fastaStr =
"> 1KQ1.A\n" +
"mianeniqdkalenfkanqtevtvfflngFQ.MKGVIEEYDK.....YVVSLNsqgkQHLIYKh......\n" +
".......................AISTYTVetegqastesee\n" +
"> 1C4Q.D\n" +
"............................tPDcVTGKVEYTKYndddtFTVKVG....DKELATnranlqs\n" +
"lllsaqitgmtvtiktnachnggGFSEVIFr...........\n";
InputStream fasta;
try {
fasta = new ByteArrayInputStream(fastaStr.getBytes("UTF-8"));
} catch (UnsupportedEncodingException e) {
e.printStackTrace();
return;
}
// Create a header parser to parse the header lines into valid structure accessions.
// The resulting accession can be anything interpretable by AtomCache.getStructure.
// Possible Examples: "4HHB" (whole structure), "d4hhba_" (SCOP domain),
// "4HHB.A:1-15" (residue range)
// For this example, the built-in fasta parser will extract the correct accession.
SequenceHeaderParserInterface headerParser;
headerParser = new GenericFastaHeaderParser();
// Create AtomCache to fetch structures from the PDB
AtomCache cache = new AtomCache();
// Create SequenceCreator. This converts a String to a ProteinSequence
AminoAcidCompoundSet aaSet = AminoAcidCompoundSet.getAminoAcidCompoundSet();
SequenceCreatorInterface creator;
creator = new CasePreservingProteinSequenceCreator(aaSet);
// parse file
FastaStructureParser parser = new FastaStructureParser(
fasta, headerParser, creator, cache);
try {
parser.process();
} catch (IOException e) {
e.printStackTrace();
return;
} catch (StructureException e) {
e.printStackTrace();
return;
}
ResidueNumber[][] residues = parser.getResidues();
ProteinSequence[] sequences = parser.getSequences();
Structure[] structures = parser.getStructures();
// Set lowercase residues to null too
for(int structNum = 0; structNum