org.geneweaver.io.reader.GTExSampleReader Maven / Gradle / Ivy
/*-
*
* Copyright 2018, 2020 The Jackson Laboratory Inc.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
* @author Matthew Gerring
*/
package org.geneweaver.io.reader;
import java.util.Map;
import org.geneweaver.domain.Entity;
import org.geneweaver.domain.Sample;
/**
*
Example of GTEx sample file.
@see https://storage.googleapis.com/gtex_analysis_v8/annotations/GTEx_Analysis_v8_Annotations_SampleAttributesDS.txt
SAMPID SMATSSCR SMCENTER SMPTHNTS SMRIN SMTS SMTSD SMUBRID SMTSISCH SMTSPAXSMNABTCH SMNABTCHT SMNABTCHD SMGEBTCH SMGEBTCHD SMGEBTCHT SMAFRZE SMGTC SME2MPRSMCHMPRS SMNTRART SMNUMGPS SMMAPRT SMEXNCRT SM550NRM SMGNSDTC SMUNMPRT SM350NRM SMRDLGTH SMMNCPB SME1MMRT SMSFLGTH SMESTLBS SMMPPD SMNTERRT SMRRNANSMRDTTL SMVQCFL SMMNCV SMTRSCPT SMMPPDPR SMCGLGTH SMGAPPCT SMUNPDRD SMNTRNRSMMPUNRT SMEXPEFF SMMPPDUN SME2MMRT SME2ANTI SMALTALG SME2SNSE SMMFLGTSME1ANTI SMSPLTRD SMBSMMRT SME1SNSE SME1PCTS SMRRNART SME1MPRT SMNUM5CSMDPMPRT SME2PCTS
GTEX-1117F-0003-SM-58Q7G B1 Blood Whole Blood 0013756 1188 BP-38516 DNA isolation_Whole Blood_QIAGEN Puregene (Manual) 05/02/2013 LCSET-4574 01/15/2014 Standard Exome Sequencing v3 (ICE) WES
GTEX-1117F-0003-SM-5DWSB B1 Blood Whole Blood 0013756 1188 BP-38516 DNA isolation_Whole Blood_QIAGEN Puregene (Manual) 05/02/2013 GTEx_OM25_Dec_01 01/28/2014 Illumina OMNI SNP Array OMNI
GTEX-1117F-0003-SM-6WBT7 B1 Blood Whole Blood 0013756 1188 BP-38516 DNA isolation_Whole Blood_QIAGEN Puregene (Manual) 05/02/2013 LCSET-6056 09/20/2014 PCR+ 30x Coverage WGS v2 (HiSeqX) WGS
* @author gerrim
*
* @param
*/
class GTExSampleReader extends LineIteratorReader {
/**
* Create the reader by setting its data
*
* @param request
* @throws ReaderException
*/
@SuppressWarnings("unchecked")
@Override
public GTExSampleReader init(ReaderRequest request) throws ReaderException {
super.setup(request);
setDelimiter("\\t");
return this;
}
private Map indices;
@SuppressWarnings("unchecked")
@Override
protected N create(String line) throws ReaderException {
String[] segs = line.split(getDelimiter());
if (line.startsWith("SAMPID")) {
indices = parseIndices(segs);
return null; // It's a header.
}
Sample ret = new Sample();
ret.setTissueGroup(segs[indices.get("smts")]);
ret.setTissueName(segs[indices.get("smtsd")]);
ret.trim();
return (N)ret;
}
}