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Merge branch 'master' of github.com:biojava/biojava
# Conflicts: # biojava-modfinder/src/test/java/org/biojava/nbio/protmod/phosphosite/TestAcetylation.java
2 parents 9f98ae6 + 55926e2 commit fe092ee

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‎CHANGELOG‎

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‎CHANGELOG.md‎

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BioJava 5.0.0
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=============
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unreleased
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- For short structure selections (e.g. 1abc.A:1-100), ligands within 5A will be included
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BioJava 4.2.5
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=============
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release date: December 7th 2016
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This release contains [30](https://github.com/biojava/biojava/compare/biojava-4.2.4...biojava-4.2.5) commits from 7 contributors.
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### Bug fixes
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* Fix for new phosphositeplus.org format, #610
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* org.biojava.nbio.genome.parsers.gff.Location union() and intersect() now work correctly, #355
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* Minor addition of crystallographic metadata fields to handle legacy PDB entries
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* Jmol interchange format is now mmCIF, allowing for multiletter chain ids
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* Update to latest jmol 14.6.2_2016.08.28
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* A few minor bug fixes
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BioJava 4.2.4
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=============
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release date: July 29th 2016
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This release contains over [17](https://github.com/biojava/biojava/compare/biojava-4.2.3...biojava-4.2.4) commits from 4 contributors.
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### Bug fixes
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* NCBI links now using https (see [NCBI's announcement](http://www.ncbi.nlm.nih.gov/news/06-10-2016-ncbi-https/) )
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* CATH links redirected to new server http://release.cathdb.info/
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* SCOP default location now points to the Berkeley server after demise of Scop at MRC LMB
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* Fixed important bug in mmCIF writing where structures with multiple models were written with identical coordinates
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* Fixed bug in Group cloning where chemical components weren't cloned
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* Added utility class for Chromosome mapping
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BioJava 4.2.3
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=============
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release date: July 28th 2016
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This release contains over [13](https://github.com/biojava/biojava/compare/biojava-4.2.2...biojava-4.2.3) commits from 2 contributors.
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### Bug fixes
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* mmCIF file writing: special fields (e.g. containing hyphens) are now correctly written
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* General improvements in mmCIF file read and write
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BioJava 4.2.2
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=============
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release date: June 14th 2016
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This release contains over [31](https://github.com/biojava/biojava/compare/biojava-4.2.1...biojava-4.2.2) commits from 5 contributors.
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### Bug fixes
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This is a bug-fix release
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* CE-Symm features and bug fixes
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- Better data structures for symmetry axes (particularly for hierarchical symmetry)
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- Fix bug with symmetry axis positioning
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- Optimization includes all symmetry repeats for hierarchical symmetry
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* Update of protein modifications to latest version,
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- including new glycans and chromophores
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- Updating naming definitions to latest conventions
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BioJava 4.2.1
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=============
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release date: May 3rd 2016
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This release contains over [31](https://github.com/biojava/biojava/compare/biojava-4.2.0...biojava-4.2.1) commits from 7 contributors.
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### Bug fixes
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Biojava-structure
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- Nucleotide bonds are now generated
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- BIO: identifiers are now correctly handled
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- Several fixes for CE-Symm
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- Substructures now contain seqres groups (isse #449)
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- Structures containing insertion codes are now written correctly to mmCIF
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- AtomCache now uses the correct default parsing parameters (issue #455)
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- Fixed problem with some atom charges that weren't being added
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- CATH updated to 4.0.0
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- Better ECOD javadocs (issue #452)
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Biojava-structure-gui
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- Removed javaws dependency (issue #459)
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BioJava 4.2.0
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=============
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release date: March 10th 2016
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This release contains over [750](https://github.com/biojava/biojava/compare/6f8d796fee92edbbcd001c33cdae4f15c5480741...biojava-4.2.0) commits from 16 contributors.
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### New Features
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BioJava 4.2.0 offers many new features, as well several bug-fixes.
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General
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- Requires Java 7
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- Better logging with SLF4J
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Biojava-Core
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- New SearchIO framework including blast xml parser
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Biojava-structure
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- Secondary structure assignment (DSSP compatible)
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- Multiple Structure Alignments
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- New MultipleStructureAlignment datastructure supporting flexible and order-independent alignments
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- MultipleMC algorithm
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- Can use any pairwise StructureAlignment implementation
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- serialize and parse multiple structure alignments as XML files, output as Text, FatCat, FASTA, Rotation Matrices, etc.
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- More complete mmCIF and cif parsing
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- Parse bonds, sites, charges
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- Better support for non-deposited pdb and mmcif files
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- Include CE-Symm algorithm for finding internal symmetry (Myers-Turnbull, 2014)
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- Replaced internal graph datastructures with Jgraph
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- Unified StructureIdentifier framework
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- Improved chemical component framework, now by default providing full chemical description by using DownloadChemCompProvider
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- Optimised memory usage of Residue/Atoms
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Biojava-structure-gui
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- MultipleAlignmentGUI for visualizing Multiple Structure Alignments with Jmol
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- SymmetryDisplay for visualizing internal symmetry
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Biojava-Phylo
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- Use Forester 1.038
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- Significant bug fixes
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- use SubstitutionMatrices in the core module (instead of imported Jalview matrices),
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- use Sequence and Compound classes from the alignment module
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- provide some Wrapper methods to communicate with forester,
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- decouple distance matrix calculation from tree constructor,
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- provide methods for common distance matrix calculations and framework for user-defined distances,
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- update the forester version to have the correct NJ tree constructor
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AND
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- correct some of the tree evaluator statistics.
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‎biojava-modfinder/src/main/java/org/biojava/nbio/phosphosite/Dataset.java‎

Lines changed: 13 additions & 37 deletions
Original file line numberDiff line numberDiff line change
@@ -21,10 +21,14 @@
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package org.biojava.nbio.phosphosite;
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import org.biojava.nbio.structure.align.util.AtomCache;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import java.io.*;
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import java.net.URL;
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import java.nio.channels.FileChannel;
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import java.nio.file.Files;
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import java.nio.file.StandardCopyOption;
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import java.util.ArrayList;
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import java.util.List;
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*/
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public class Dataset {
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private static final Logger logger = LoggerFactory.getLogger(Dataset.class);
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public static final String ACETYLATION = "http://www.phosphosite.org/downloads/Acetylation_site_dataset.gz";
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public void download(){
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System.out.println("Downloading data from www.phosposite.org. Data is under CC-BY-NC-SA license. Please link to site and cite: ");
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System.out.println("Hornbeck PV, Kornhauser JM, Tkachev S, Zhang B, Skrzypek E, Murray B, Latham V, Sullivan M (2012) PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 40(Database issue), D261–70.");
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logger.warn("Downloading data from www.phosposite.org. Data is under CC-BY-NC-SA license. Please link to site and cite: ");
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logger.warn("Hornbeck PV, Kornhauser JM, Tkachev S, Zhang B, Skrzypek E, Murray B, Latham V, Sullivan M (2012) PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 40(Database issue), D261–70.");
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File dir = getLocalDir();
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}
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private void downloadFile(URL u, File localFile) throws IOException {
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public void downloadFile(URL u, File localFile) throws IOException {
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System.out.println("Downloading " + u);
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logger.info("Downloading " + u);
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File tmp = File.createTempFile("tmp","phosphosite");
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public static void copyFile(File src, File dst) throws IOException
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{
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// TODO: upgrade to Java 7:
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Files.copy(src.toPath(), dst.toPath(), StandardCopyOption.REPLACE_EXISTING);
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// Files.copy(src.toPath(), dst.toPath(), StandardCopyOption.REPLACE_EXISTING);
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long p = 0, dp, size;
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FileChannel in = null, out = null;
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try
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{
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if (!dst.exists()) dst.createNewFile();
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in = new FileInputStream(src).getChannel();
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out = new FileOutputStream(dst).getChannel();
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size = in.size();
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while ((dp = out.transferFrom(in, p, size)) > 0)
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{
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p += dp;
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}
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}
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finally {
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try
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{
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if (out != null) out.close();
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}
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finally {
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if (in != null) in.close();
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}
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}
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}
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try {
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231206
for (File f : ds.getLocalFiles()) {
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System.out.println(f.getAbsoluteFile());
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logger.info(f.getAbsolutePath());
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List<Site> sites = Site.parseSites(f);
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logger.info("Got " + sites.size() + " sites");
237213
for (Site s : sites) {
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if (s.getUniprot().equals("P50225") || s.getUniprot().equals("P48025")) {
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System.out.println(s);
215+
logger.info(s.toString());
240216
}
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}
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‎biojava-modfinder/src/main/java/org/biojava/nbio/phosphosite/Site.java‎

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int proteinIndex = -1;
5858
int uniprotIndex = -1;
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int modTypeIndex = -1;
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int residueIndex = -1;
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int orgIndex = -1;
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int groupIndex = -1;
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int geneIndex = -1;
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boolean inHeader = true;
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6767
while ((line = buf.readLine()) != null){
68-
if ( line.startsWith("PROTEIN")) {
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if ( line.startsWith("GENE") ||
69+
line.startsWith("PROTEIN")) {
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headerFields = parseHeaderFields(line);
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7273
proteinIndex = headerFields.indexOf("PROTEIN");
7374
uniprotIndex = headerFields.indexOf("ACC_ID");
74-
modTypeIndex = headerFields.indexOf("MOD_TYPE");
7575
residueIndex = headerFields.indexOf("MOD_RSD");
76-
orgIndex = headerFields.indexOf("ORG");
76+
orgIndex = headerFields.indexOf("ORGANISM");
7777
groupIndex = headerFields.indexOf("SITE_GRP_ID");
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geneIndex = headerFields.indexOf("GENE");
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inHeader = false;
8081
continue;
@@ -95,19 +96,25 @@ public static List<Site> parseSites(File f) throws IOException {
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String protein = spl[proteinIndex];
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String uniprot = spl[uniprotIndex];
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//String geneSymb = spl[2];
99-
//String chrLoc = spl[3];
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String modType = spl[modTypeIndex];
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101100
String residue = spl[residueIndex];
101+
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String[] resSpl = residue.split("-");
103+
String modType = null;
104+
if ( resSpl.length == 2) {
105+
106+
modType = resSpl[1];
107+
}
102108
String group = spl[groupIndex];
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104110
String organism = spl[orgIndex];
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112+
String geneSymb = spl[geneIndex];
113+
106114
Site s = new Site();
107115
s.setProtein(protein);
108116
s.setUniprot(uniprot);
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//s.setGeneSymb(geneSymb);
110-
//s.setChrLoc(chrLoc);
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s.setGeneSymb(geneSymb);
111118
s.setModType(modType);
112119
s.setResidue(residue);
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s.setGroup(group);

‎biojava-modfinder/src/test/java/org/biojava/nbio/protmod/phosphosite/TestAcetylation.java‎

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Original file line numberDiff line numberDiff line change
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1414
import static org.junit.Assert.assertTrue;
1515
import static org.junit.Assert.fail;
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17-
/** Makes sure there is a local installation of the Acetyaltion site file from Phosphosite and
17+
18+
/** Makes sure there is a local installation of the Acetylation site file from Phosphosite and
1819
* tests if it can get parsed by the parser.
1920
*
2021
* Created by andreas on 11/29/16.
@@ -27,21 +28,18 @@ public class TestAcetylation {
2728
*
2829
*/
2930
@Before
30-
public void setUp(){
31+
public void setUp() throws IOException{
3132

3233
Dataset ds = new Dataset();
3334

3435
String f = Dataset.ACETYLATION;
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3637
File localFile = getLocalFileName(f);
3738

38-
try {
39-
if (!localFile.exists()) {
40-
ds.downloadFile(new URL(f), localFile);
41-
}
42-
} catch (IOException e) {
43-
e.printStackTrace();
39+
if (!localFile.exists()) {
40+
ds.downloadFile(new URL(f), localFile);
4441
}
42+
4543
}
4644

4745
/** returns the local file name where the Acetylation file will get cached locally.
@@ -70,26 +68,19 @@ private File getLocalFileName(String phosphoSiteFileLocation){
7068
*
7169
*/
7270
@Test
73-
public void testAcetylation() {
74-
75-
try {
71+
public void testAcetylation() throws IOException {
7672

77-
File localFile = getLocalFileName(Dataset.ACETYLATION);
73+
File localFile = getLocalFileName(Dataset.ACETYLATION);
7874

79-
List<Site> sites = Site.parseSites(localFile);
75+
List<Site> sites = Site.parseSites(localFile);
8076

81-
assertTrue(sites.size() > 0);
77+
assertTrue(sites.size() > 0);
8278

83-
for (Site s : sites) {
79+
for (Site s : sites) {
8480

85-
assertTrue(s.getResidue() != null);
81+
assertTrue(s.getResidue() != null);
8682

87-
}
88-
89-
90-
} catch (Exception e) {
91-
e.printStackTrace();
92-
fail(e.getMessage());
9383
}
84+
9485
}
9586
}

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