Skip to content

parser for Pro ontology alterative names (PAF.txt) #11

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
ekwhite wants to merge 1 commit into
base: master
Choose a base branch
from
Open

parser for Pro ontology alterative names (PAF.txt) #11

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
254 changes: 254 additions & 0 deletions ...-fileparsers/src/main/java/edu/ucdenver/ccp/datasource/fileparsers/pro/PAFFileParser.java
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,254 @@
package edu.ucdenver.ccp.datasource.fileparsers.pro;

/*
* #%L
* Colorado Computational Pharmacology's common module
* %%
* Copyright (C) 2012 - 2015 Regents of the University of Colorado
* %%
* Redistribution and use in source and binary forms, with or without modification,
* are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer.
*
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* 3. Neither the name of the Regents of the University of Colorado nor the names of its contributors
* may be used to endorse or promote products derived from this software without
* specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
* IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
* INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
* BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
* LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
* OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
* OF THE POSSIBILITY OF SUCH DAMAGE.
* #L%
*/

import java.io.File;
import java.io.IOException;
import java.util.Set;
import java.util.HashSet;



import edu.ucdenver.ccp.common.download.FtpDownload;
import edu.ucdenver.ccp.common.file.CharacterEncoding;
import edu.ucdenver.ccp.common.file.reader.Line;
import edu.ucdenver.ccp.common.file.reader.StreamLineReader;
import edu.ucdenver.ccp.common.ftp.FTPUtil.FileType;
import edu.ucdenver.ccp.common.string.StringUtil;
import edu.ucdenver.ccp.common.string.StringConstants;
import edu.ucdenver.ccp.common.string.StringUtil.RemoveFieldEnclosures;

import edu.ucdenver.ccp.datasource.fileparsers.SingleLineFileRecordReader;
import edu.ucdenver.ccp.datasource.identifiers.DataSourceIdentifier;
import edu.ucdenver.ccp.datasource.identifiers.ProbableErrorDataSourceIdentifier;
import edu.ucdenver.ccp.datasource.identifiers.UnknownDataSourceIdentifier;
import edu.ucdenver.ccp.datasource.identifiers.ebi.uniprot.UniProtID;
import edu.ucdenver.ccp.datasource.identifiers.ebi.interpro.PirSfID;
import edu.ucdenver.ccp.datasource.identifiers.ebi.interpro.PfamID;
import edu.ucdenver.ccp.datasource.identifiers.ebi.interpro.PantherID;
import edu.ucdenver.ccp.datasource.identifiers.hgnc.HgncID;
import edu.ucdenver.ccp.datasource.identifiers.mgi.MgiGeneID;
import edu.ucdenver.ccp.datasource.identifiers.obo.GeneOntologyID;
import edu.ucdenver.ccp.datasource.identifiers.obo.ProteinOntologyId;
import edu.ucdenver.ccp.datasource.identifiers.rgd.RgdID;

/**
* File parser for Protein Ongology promapping.txt file.
*
* @author Yuriy Malenkiy
*
*/
public class PAFFileParser extends SingleLineFileRecordReader<PAFRecord> {

public static final String IS_A_RELATION = "is_a";
public static final String EXACT_RELATION = "exact";

private static final String HEADER = "PRO_ID\tObject_term\tObject_syny\tModifier\tRelation\tOntology_ID\tOntology_term\tRelative_to\tInteraction_with\tEvidence_source\tEvidence_code\tTaxon\tInferred_from DB_ID\tAssigned_by\tComment";

public static final CharacterEncoding FILE_ENCODING = CharacterEncoding.US_ASCII;

@FtpDownload(server = "ftp.pir.georgetown.edu", path = "databases/ontology/pro_obo/old_files/tmp1/", filename = "PAF.txt", filetype = FileType.ASCII)
private File mappingFile;

/**
* Constructor.
*
* @param dataFile
* @param encoding
* @param skipLinePrefix
* @throws IOException
*/
public PAFFileParser(File dataFile, CharacterEncoding encoding) throws IOException {
super(dataFile, encoding);
}

/**
* Default constructor
*
* @param workDirectory
* @param clean
* @throws IOException
*/
public PAFFileParser(File workDirectory, boolean clean) throws IOException {
super(workDirectory, FILE_ENCODING, null, clean);
}

@Override
protected StreamLineReader initializeLineReaderFromDownload(CharacterEncoding encoding, String skipLinePrefix)
throws IOException {
return new StreamLineReader(mappingFile, encoding, skipLinePrefix);
}

/*
* (non-Javadoc)
*
* @see
* edu.ucdenver.ccp.fileparsers.SingleLineFileRecordReader#parseRecordFromLine
* (edu.ucdenver. ccp.common.file.reader.LineReader.Line)
*/
@Override
protected PAFRecord parseRecordFromLine(Line line) {
String text = line.getText();
PAFRecord r = null;

if (text.startsWith("PR:")) {

String[] tokens = text.split("\t");
int k = 0;
ProteinOntologyId fromId = new ProteinOntologyId(tokens[0].trim());
String modifier = "";
String relationName = "";
DataSourceIdentifier<?> relationOntologyId = null;
String relationOntologyTerm = "";
DataSourceIdentifier<?> referenceProtein = null;
String evidenceCode = "";
String taxon = "";
String date = "";
String annotatorInitials = "";
String comment = "";

String name = tokens[1].trim();

Set<String> nameSynonyms = new HashSet<String>();
for (String syn : StringUtil.delimitAndTrim(tokens[2], StringConstants.VERTICAL_LINE, null,
RemoveFieldEnclosures.FALSE)) {
nameSynonyms.add(new String(syn));
}
if (tokens[3].length() > 0) {
modifier = new String(tokens[3].trim());
}

if (tokens[4].length() > 0) {
relationName = new String(tokens[4].trim());
}
if (tokens[5].length() > 0) {
relationOntologyId = resolveId(tokens[5].trim());
}
if (tokens[6].length() > 0) {
relationOntologyTerm = new String(tokens[6].trim());
}
if (tokens[7].length() > 0) {
referenceProtein = resolveId(tokens[7].trim());
}
Set<DataSourceIdentifier<?>> interactionPartners = new HashSet<DataSourceIdentifier<?>>();
if (tokens[8].length() > 0) {
for (String partner : StringUtil.delimitAndTrim(tokens[8], StringConstants.VERTICAL_LINE, null,
RemoveFieldEnclosures.FALSE)) {
DataSourceIdentifier<?> intPartner = resolveId(partner);
interactionPartners.add(intPartner);
}
}
Set<DataSourceIdentifier<?>> evidenceSource = new HashSet<DataSourceIdentifier<?>>();
if (tokens[9].length() > 0) {
for (String src : StringUtil.delimitAndTrim(tokens[9], StringConstants.VERTICAL_LINE, null,
RemoveFieldEnclosures.FALSE)) {
DataSourceIdentifier<?> evid = resolveId(src);
evidenceSource.add(evid);
}
}



if (tokens[10].length() > 0) {
evidenceCode = tokens[10].trim();
}
if (tokens[11].length() > 0) {
taxon = tokens[11].trim();
}
Set<DataSourceIdentifier<?>> inferredFrom = new HashSet<DataSourceIdentifier<?>>();
if (tokens[12].length() > 0) {
for (String src : StringUtil.delimitAndTrim(tokens[12], StringConstants.VERTICAL_LINE, null,
RemoveFieldEnclosures.FALSE)) {
DataSourceIdentifier<?> evid = resolveId(src);
inferredFrom.add(evid);
}
}
Set<DataSourceIdentifier<?>> inferredFromDB = new HashSet<DataSourceIdentifier<?>>();
if (tokens[13].length() > 0) {
for (String src : StringUtil.delimitAndTrim(tokens[13], StringConstants.VERTICAL_LINE, null,
RemoveFieldEnclosures.FALSE)) {
DataSourceIdentifier<?> evid = resolveId(src);
inferredFromDB.add(evid);
}
}
if (tokens[14].length() > 0) {
date = tokens[14].trim();
}

if (tokens[15].length() > 0) {
annotatorInitials = tokens[15].trim();
}


r = new PAFRecord(fromId, name, nameSynonyms, modifier, relationName, relationOntologyId,
relationOntologyTerm, referenceProtein, interactionPartners, evidenceSource,
evidenceCode, taxon, inferredFrom, inferredFromDB, date, annotatorInitials, "",
line.getByteOffset(), line.getLineNumber());
}

return r;
}

private DataSourceIdentifier<?> resolveId(String idStr) {
try {
if (idStr.startsWith("MGI:")) {
return new MgiGeneID(idStr);
}
if (idStr.startsWith("Pfam:")) {
return new PfamID(StringUtil.removePrefix(idStr, "Pfam:"));
}
if (idStr.startsWith("GO:")) {
return new GeneOntologyID(idStr);
}
if (idStr.startsWith("RGD:")) {
return new RgdID(StringUtil.removePrefix(idStr, "RGD:"));
}
if (idStr.startsWith("PIRSF:")) {
return new PirSfID(StringUtil.removePrefix(idStr, "PIRSF:"));
}
if (idStr.startsWith("PANTHER:")) {
return new PantherID(StringUtil.removePrefix(idStr, "PANTHER:"));
}
if (idStr.startsWith("HGNC:")) {
return new HgncID(idStr);
}
if (idStr.startsWith("UniProtKB:")) {
return new UniProtID(StringUtil.removePrefix(idStr, "UniProtKB:"));
}
} catch (IllegalArgumentException e) {
return new ProbableErrorDataSourceIdentifier(idStr, null, e.getMessage());
}
return new UnknownDataSourceIdentifier(idStr, null);
}
}
Loading