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/*-
*
* 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 org.apache.poi.ss.usermodel.Cell;
import org.apache.poi.ss.usermodel.Row;
import org.geneweaver.domain.Anchor;
import org.geneweaver.domain.AnchoredEntity;
import org.geneweaver.domain.ChromatinInteraction;
import org.geneweaver.domain.ExperimentMetadata;
/**
Process the spreadsheet containing short/long range chromatin interactions in
human MCF7 and K562 cells from study PMID:22265404.
Threshold based on significance (FDR < 0.05), remove irrelevant fields, and return
a dataframe containing the results.
inputs
fp: input filepath
sheet: optional value indicating what sheet in the excel file to parse
These are the sheets, name and indices, in the excel file:
Summary 0
MCF7 pilot peaks 1
All pilot peaks 2
K562 saturated peaks 3
MCF7 saturated peaks 4
MCF7 pilot interactions 5
All pilot interactions 6
K562 saturated interactions #1 7
K562 saturated interactions #2 8
MCF7 saturated interactions 9
We want sheets 5, 7, 8, 9.
* @author gerrim
*
* @param
*/
class ChiapetReader extends AbstractXlsReader {
@SuppressWarnings("unchecked")
@Override
protected N create(Row row) {
Class concrete = getConcreteClass();
try {
if (concrete==null) concrete = (Class)ChromatinInteraction.class;
} catch (RuntimeException ne) {
throw new IllegalArgumentException("Please set the concrete class on "+getClass().getSimpleName(), ne);
}
Cell cell = row.getCell(0);
if (cell==null) return null;
String chr = cell.getStringCellValue();
if (chr==null) return null;
if (!chr.matches("chr(\\d+|X|Y|M)")) return null; // Null is filtered from the stream.
if (concrete == ChromatinInteraction.class) {
ChromatinInteraction c = new ChromatinInteraction();
c.setChr(chr);
ExperimentMetadata meta = getMeta();
if (meta!=null) meta.setChr(chr);
c.setMeta(meta);
c.setLeft(createAnchor(row, 0,1,2));
c.setRight(createAnchor(row, 3,4,5));
c.setPetCount((int)Math.round(row.getCell(6).getNumericCellValue()));
c.setP(row.getCell(7).getNumericCellValue());
c.setFdr(row.getCell(8).getNumericCellValue());
String overlap = row.getCell(9)!=null ? row.getCell(9).getStringCellValue() : null;
c.setOverlapDNAPET("Yes".equalsIgnoreCase(overlap));
return (N)c;
} else if (concrete == Anchor.class) {
return (N)createAnchor(row, 0,1,2,3);
}
throw new IllegalArgumentException("Class "+getConcreteClass()+" cannot be pared using "+getClass().getSimpleName());
}
private Anchor createAnchor(Row row, int i, int j, int k, int l) {
return new Anchor(row.getCell(i).getStringCellValue(),
(int)Math.round(row.getCell(j).getNumericCellValue()),
(int)Math.round(row.getCell(k).getNumericCellValue()),
(int)Math.round(row.getCell(l).getNumericCellValue()));
}
private Anchor createAnchor(Row row, int i, int j, int k) {
return new Anchor(row.getCell(i).getStringCellValue(),
(int)Math.round(row.getCell(j).getNumericCellValue()),
(int)Math.round(row.getCell(k).getNumericCellValue()));
}
}
