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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 java.io.IOException;
import java.util.Arrays;
import java.util.function.Function;
import java.util.stream.Stream;
import org.geneweaver.domain.Entity;
import org.geneweaver.domain.HomologGene;
import org.geneweaver.io.connector.HomologConnector;
/**
*
*
Homologene records from @see http://www.informatics.jax.org/downloads/reports/HOM_MouseHumanSequence.rpt
Example:
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
Or newer file format:
DB Class Key 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
38710983 mouse, laboratory 10090 Gdnf 14573 MGI:107430 Chr15 3.8 cM Chr15:7840327-7867056(+) NM_001301357,NM_010275,NM_001301333,NM_001301332 NP_001288286,NP_001288262,NP_034405,NP_001288261 P48540
38710983 human 9606 GDNF 2668 HGNC:4232 OMIM:600837 Chr5 p13.2 Chr5:37812677-37840044(-) NM_199231,NM_001278098,NM_199234,NM_001190469,NM_001190468,NM_000514 NP_001265027,NP_000505,NP_001177397,NP_001177398,XP_016864826,XP_011512332,NP_954701 P39905
38710984 mouse, laboratory 10090 Rrm1 20133 MGI:98180 Chr7 54.72 cM Chr7:102090902-102118978(+) NM_009103 NP_033129 P07742
38710984 human 9606 RRM1 6240 HGNC:10451 OMIM:180410 Chr11 p15.4 Chr11:4094685-4138925(+) NM_001033,NM_001318065,NM_001330193,NM_001318064 NP_001024,NP_001317122,NP_001304994,NP_001304993 P23921
38710985 mouse, laboratory 10090 Hoxd12 15432 MGI:96204 Chr2 44.13 cM Chr2:74505357-74508049(+) NM_008274 NP_032300 P23812
38710985 human 9606 HOXD12 3238 HGNC:5135 OMIM:142988 Chr2 q31.1 Chr2:176099802-176100760(+) NM_021193 NP_067016 P35452
e.g. for human
HomoloGene ID 3
Common Organism Name human
NCBI Taxon ID 9606
Symbol ACADM
EntrezGene ID 34
Mouse MGI ID HGNC:89
HGNC ID OMIM Gene ID OMIM:607008
Genetic Location Chr1 p31.1
Genomic Coordinates (mouse: , human: ) Chr1:75724347-75763679(+)
Nucleotide RefSeq IDs NM_001286043,NM_000016,NM_001127328,NM_001286042,NM_001286044
Protein RefSeq IDs NP_001120800,NP_001272971,NP_001272972,NP_001272973,NP_000007
SWISS_PROT IDs P11310
e.g. for mouse
HomoloGene ID 12
Common Organism Name mouse, laboratory
NCBI Taxon ID 10090
Symbol Adsl
EntrezGene ID 11564
Mouse MGI ID MGI:103202
HGNC ID OMIM Gene ID
Genetic Location Chr11 59.01 cM
Genomic Coordinates (mouse: , human: ) Chr11:94962791-94976327(-)
Nucleotide RefSeq IDs XM_011248836,NM_009161
Protein RefSeq IDs P_033187,XP_011247138
SWISS_PROT IDs P82350
*
* @author gerrim
*
*/
class HomologGeneReader extends LineIteratorReader {
/**
* Instantiates a new gene reader.
*
* @param request
* @throws IOException
*/
@Override
public HomologGeneReader init(ReaderRequest request) throws ReaderException {
super.setup(request);
setDelimiter("\t+"); // Must be a tab only as spaces are allowed
return this;
}
@Override
public Function> getDefaultConnector() {
return new HomologConnector<>(); // Creates connections for two consecutive lines.
}
@Override
protected T create(String line) throws ReaderException {
if (line.startsWith("HomoloGene ID")) return null;
if (line.startsWith("DB Class Key")) return null;
String[] rec = line.split(getDelimiter());
HomologGene gene = new HomologGene();
gene.setSource(request.getSource());
int i = 0;
gene.setHid(Long.parseLong(rec[i++]));
gene.setOrganismName(rec[i++]);
gene.setTaxonId(Long.parseLong(rec[i++]));
gene.setSymbol(rec[i++]);
gene.setEntrezId(Long.parseLong(rec[i++]));
gene.setMgiId(rec[i++]);
boolean isHum = gene.getOrganismName().equalsIgnoreCase("human");
if (isHum) {
if (rec.length>6) gene.setHgncId(rec[i++]);
}
// Sometimes data at the end is missing.
if (isHum) {
if (rec.length>7) gene.setLocation(rec[i++]);
if (rec.length>8) gene.setCoords(rec[i++]);
if (rec.length>9) gene.setNucelotideSeqIds(Arrays.asList(rec[i++].split(",")));
if (rec.length>10) gene.setProteinSeqIds(Arrays.asList(rec[i++].split(",")));
if (rec.length>11) gene.setSwissProtIds(Arrays.asList(rec[i++].split(",")));
} else {
if (rec.length>6) gene.setLocation(rec[i++]);
if (rec.length>7) gene.setCoords(rec[i++]);
if (rec.length>8) gene.setNucelotideSeqIds(Arrays.asList(rec[i++].split(",")));
if (rec.length>9) gene.setProteinSeqIds(Arrays.asList(rec[i++].split(",")));
if (rec.length>10) gene.setSwissProtIds(Arrays.asList(rec[i++].split(",")));
}
return (T)gene;
}
}
