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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.connector;
import java.io.PrintStream;
import java.util.Collection;
import java.util.LinkedList;
import java.util.concurrent.TimeUnit;
import java.util.function.Function;
import java.util.stream.Stream;
import org.geneweaver.domain.Entity;
import org.geneweaver.domain.Homolog;
import org.geneweaver.domain.HomologGene;
import org.neo4j.ogm.session.Session;
import com.google.common.cache.Cache;
import com.google.common.cache.CacheBuilder;
/**
* It is designed to be used with parallel streams which is why a
* cache rather than a reference is used.
*
* PLEASE USE HomologFunction to get the GeneID before using HomologConnector to make the connection between
* mouse and human genes.
*
*
HomoloGene ID Common Organism Name NCBI Taxon ID Symbol EntrezGene ID Mouse MGI ID HGNC ID OMIM Gene ID Genetic Location Genomic Coordinates (mouse: , human: ) Nucleotide RefSeq IDs Protein RefSeq IDs SWISS_PROT IDs
3 mouse, laboratory 10090 Acadm 11364 MGI:87867 Chr3 78.77 cM Chr3:153922357-153944632(-) NM_007382 NP_031408 P45952
3 human 9606 ACADM 34 HGNC:89 OMIM:607008 Chr1 p31.1 Chr1:75724347-75763679(+) NM_001286043,NM_000016,NM_001127328,NM_001286042,NM_001286044 NP_001120800,NP_001272971,NP_001272972,NP_001272973,NP_000007 P11310
5 mouse, laboratory 10090 Acadvl 11370 MGI:895149 Chr11 42.96 cM Chr11:70010183-70015411(-) NM_017366 NP_059062 P50544
5 human 9606 ACADVL 37 HGNC:92 OMIM:609575 Chr17 p13.1 Chr17:7217125-7225267(+) NM_000018,NM_001033859,NM_001270448,NM_001270447 NP_001029031,NP_001257377,XP_006721579,XP_011522131,XP_011522132,NP_000009,XP_024306509,NP_001257376 P49748
6 mouse, laboratory 10090 Acat1 110446 MGI:87870 Chr9 29.12 cM Chr9:53580522-53610350(-) NM_144784 NP_659033 Q8QZT1
6 human 9606 ACAT1 38 HGNC:93 OMIM:607809 Chr11 q22.3 Chr11:108121531-108148168(+) NM_001386689,NM_001386688,NM_001386687,NM_001386686,NM_001386691,NM_001386678,NM_000019,NM_001386677,NM_001386685,NM_001386682,NM_001386679,NM_001386681,NM_001386690 NP_001373615,NP_001373617,NP_001373618,NP_001373619,NP_001373620,XP_016873171,XP_024304282,NP_001373607,NP_001373606,NP_000010,NP_001373608,NP_001373610,NP_001373611,NP_001373614,NP_001373616 P24752
7 mouse, laboratory 10090 Acvr1 11477 MGI:87911 Chr2 33.05 cM Chr2:58446438-58566828(-) NM_001355049,NM_001110205,NM_001355048,NM_007394,NM_001110204,XM_006497622 NP_001341978,NP_001103675,NP_001103674,NP_001341977,NP_031420,XP_006497685 P37172
7 human 9606 ACVR1 90 HGNC:171 OMIM:102576 Chr2 q24.1 Chr2:157736446-157875880(-) NM_001347667,NM_001347666,NM_001347665,NM_001347664,NM_001347663,NM_001111067,NM_001105 NP_001334594,NP_001334595,NP_001334596,XP_006712888,XP_011510410,NP_001096,NP_001104537,NP_001334592,NP_001334593 Q04771
9 mouse, laboratory 10090 Sgca 20391 MGI:894698 Chr11 59.01 cM Chr11:94962791-94976327(-) XM_011248836,NM_009161 NP_033187,XP_011247138 P82350
9 human 9606 SGCA 6442 HGNC:10805 OMIM:600119 Chr17 q21.33 Chr17:50165517-50175932(+) NM_001135697,NM_000023 XP_011523422,NP_001129169,NP_000014,XP_024306641,XP_011523426,XP_011523425,XP_011523424,XP_011523423 Q16586
12 mouse, laboratory 10090 Adsl 11564 MGI:103202 Chr15 37.95 cM Chr15:80948490-80970946(+) NM_009634 NP_033764 P54822
12 human 9606 ADSL 158 HGNC:291 OMIM:608222 Chr22 q13.1 Chr22:40346500-40387408(+) NM_000026,NM_001363840,NM_001317923,NM_001123378 XP_016884128,XP_024307934,XP_016884129,XP_016884127,XP_016884126,XP_016884125,XP_011528282,XP_011528279,NP_001350769,NP_001304852,NP_001116850,NP_000017 P30566
* @author gerrim
*
* @param
* @param
*/
public class HomologConnector implements Connector, Function> {
/**
* We store recently created Genes by id. We look in this pool for the
* Gene corresponding to the current transcript so that we can make a link.
* Since the Gene file is quite large, we do not keep all the keys in memory
* all the time. Instead we use Guava to create a local temporary cache.
* We Cannot just save the last Gene and use it because we want to use multiple
* threads to consume lines from the file sometimes.
*/
private Cache> mouseCache = createCache();
@SuppressWarnings("unchecked")
@Override
public Stream stream(N entity, Session unused, PrintStream log) {
HomologGene hgene = (HomologGene)entity;
if (hgene.getOrganismName().toLowerCase().startsWith("mouse")) {
Collection mhols = mouseCache.getIfPresent(hgene.getHid());
if (mhols==null) {
mhols = new LinkedList<>();
mouseCache.put(hgene.getHid(), mhols);
}
mhols.add(hgene);
return (Stream)Stream.of(hgene);
} else {
Long hid = hgene.getHid();
Collection mouse = mouseCache.getIfPresent(hid);
if (mouse !=null) {
Collection ret = new LinkedList<>();
for (HomologGene hg : mouse) {
Homolog hom = new Homolog(hg.getHid(), hg.getGeneId(), hgene.getGeneId());
hom.setSource(hgene.getSource());
ret.add((E)hom);
}
ret.add((E)hgene);
return ret.stream();
} else {
return (Stream)Stream.of(hgene);
}
}
}
private Cache createCache() {
return CacheBuilder.newBuilder()
.maximumSize(1000)
.expireAfterWrite(1, TimeUnit.MINUTES)
.build();
}
@Override
public Stream apply(N t) {
return stream(t);
}
}
