/*
The MIT License (MIT)
Copyright (c) 2014 Pierre Lindenbaum
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
History:
* 2014 creation
* 2015 knime interface
*/
package com.github.lindenb.jvarkit.tools.vcffilterso;
import java.io.BufferedReader;
import java.io.File;
import java.io.IOException;
import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import java.util.stream.Collectors;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.variantcontext.VariantContextBuilder;
import htsjdk.variant.variantcontext.writer.VariantContextWriter;
import htsjdk.variant.vcf.VCFFilterHeaderLine;
import htsjdk.variant.vcf.VCFHeader;
import com.beust.jcommander.Parameter;
import com.github.lindenb.jvarkit.io.IOUtils;
import com.github.lindenb.jvarkit.lang.JvarkitException;
import com.github.lindenb.jvarkit.util.jcommander.Launcher;
import com.github.lindenb.jvarkit.util.jcommander.Program;
import com.github.lindenb.jvarkit.util.log.Logger;
import com.github.lindenb.jvarkit.util.so.SequenceOntologyTree;
import com.github.lindenb.jvarkit.util.vcf.VcfIterator;
import com.github.lindenb.jvarkit.util.vcf.predictions.AnnPredictionParser;
import com.github.lindenb.jvarkit.util.vcf.predictions.AnnPredictionParserFactory;
import com.github.lindenb.jvarkit.util.vcf.predictions.MyPredictionParser;
import com.github.lindenb.jvarkit.util.vcf.predictions.SnpEffPredictionParser;
import com.github.lindenb.jvarkit.util.vcf.predictions.SnpEffPredictionParserFactory;
import com.github.lindenb.jvarkit.util.vcf.predictions.VepPredictionParser;
import com.github.lindenb.jvarkit.util.vcf.predictions.VepPredictionParserFactory;
/**
* VCF filter on Sequence Ontology
BEGIN_DOC
## Examples
### Example 1
list the variants having a "*feature_elongation*" ( SO:0001907 ) http://www.sequenceontology.org/browser/current_release/term/SO:0001907
here the variant is selected because *stop_lost* is a children of *SO:0001907* .
```
$ curl -s -k "https://raw.github.com/arq5x/gemini/master/test/test5.vep.snpeff.vcf" | \
java -jar dist/vcffilterso.jar -A "SO:0001907" |\
grep -v "##"
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT M10475 M10478 M10500M128215
chr10 1142208 . T C 3404.30 . AC=8;AF=1.00;AN=8;CSQ=intron_variant|||ENSG00000047056|WDR37|ENST00000263150|||,downstream_gene_variant|||ENSG00000047056|WDR37|ENST00000436154|||,intron_variant|||ENSG00000047056|WDR37|ENST00000358220|||,stop_lost|Tga/Cga|* / R|ENSG00000047056|WDR37|ENST00000381329|9/9||;DP=122;Dels=0.00;EFF=DOWNSTREAM(MODIFIER||||208|WDR37|protein_coding|CODING|ENST00000436154|),INTRON(MODIFIER||||494|WDR37|protein_coding|CODING|ENST00000263150|9),INTRON(MODIFIER||||494|WDR37|protein_coding|CODING|ENST00000358220|9),STOP_LOST(HIGH|MISSENSE|Tga/Cga|*250R|249|WDR37|protein_coding|CODING|ENST00000381329|);FS=0.000;HRun=0;HaplotypeScore=2.6747;MQ=36.00;MQ0=0;QD=27.90 GT:AD:DP:GQ:PL 1/1:1,37:39:87.16:940,87,0 1/1:0,29:29:78.20:899,78,0 1/1:0,24:24:66.14:729,66,0 1/1:0,30:30:75.18:836,75,0
```
### Example 2
invert the query:
```
$ curl -s -k "https://raw.github.com/arq5x/gemini/master/test/test5.vep.snpeff.vcf" | \
java -jar dist/vcffilterso.jar -v -A "SO:0001907" |\
grep -v "##"
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT M10475 M10478 M10500M128215
chr1 145273345 . T C 289.85 . AC=3;AF=0.38;AN=8;BaseQRankSum=1.062;CSQ=missense_variant|Tct/Cct|S/P|ENSG00000213240|NOTCH2NL|ENST00000369340|4/6|benign(0.238)|tolerated(0.45),missense_variant|Tct/Cct|S/P|ENSG00000213240|NOTCH2NL|ENST00000362074|3/5|benign(0.238)|tolerated(0.45),missense_variant&NMD_transcript_variant|Tct/Cct|S/P|ENSG00000255168||ENST00000468030|3/23|benign(0.416)|tolerated(0.55),missense_variant|Tct/Cct|S/P|ENSG00000213240|NOTCH2NL|ENST00000344859|3/6|possibly_damaging(0.545)|tolerated(0.44);DP=1000;DS;Dels=0.00;EFF=EXON(MODIFIER|||||RP11-458D21.5|nonsense_mediated_decay|NON_CODING|ENST00000468030|3),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Cct|S67P|230|NOTCH2NL|protein_coding|CODING|ENST00000344859|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Cct|S67P|236|NOTCH2NL|protein_coding|CODING|ENST00000362074|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Cct|S67P|236|NOTCH2NL|protein_coding|CODING|ENST00000369340|);FS=3.974;HRun=1;HaplotypeScore=17.4275;MQ=29.25;MQ0=0;MQRankSum=-1.370;QD=0.39;ReadPosRankSum=-1.117 GT:AD:DP:GQ:PL 0/0:226,22:250:99:0,158,4259 0/1:224,24:250:5.77:6,0,5314 0/1:219,28:249:57.30:57,0,5027 0/1:215,34:250:99:269,0,3796
chr1 156011444 . T C 2523.46 . AC=4;AF=0.50;AN=8;BaseQRankSum=-0.490;CSQ=missense_variant|atA/atG|I/M|ENSG00000160803|UBQLN4|ENST00000368309|10/11|benign(0.012)|tolerated(0.3),downstream_gene_variant|||ENSG00000160803|UBQLN4|ENST00000459954|||,missense_variant|Atc/Gtc|I/V|ENSG00000160803|UBQLN4|ENST00000368307|6/7|unknown(0)|tolerated(0.88);DP=204;Dels=0.00;EFF=DOWNSTREAM(MODIFIER|||||UBQLN4|processed_transcript|CODING|ENST00000459954|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Gtc|I148V|226|UBQLN4|protein_coding|CODING|ENST00000368307|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atA/atG|I495M|601|UBQLN4|protein_coding|CODING|ENST00000368309|);FS=4.328;HRun=0;HaplotypeScore=4.3777;MQ=35.24;MQ0=0;MQRankSum=-0.101;QD=14.93;ReadPosRankSum=1.575 GT:AD:DP:GQ:PL 0/1:24,15:40:99:214,0,443 0/1:32,36:68:99:702,0,794 1/1:1,59:61:99:1656,132,0 0/0:34,1:35:69.10:0,69,717
chr5 64982321 . T C 61.12 . AC=4;AF=1.00;AN=4;CSQ=intron_variant|||ENSG00000197860|SGTB|ENST00000381007|||,intron_variant|||ENSG00000197860|SGTB|ENST00000506816|||;DP=4;Dels=0.00;EFF=INTRON(MODIFIER||||194|SGTB|protein_coding|CODING|ENST00000506816|5),INTRON(MODIFIER||||304|SGTB|protein_coding|CODING|ENST00000381007|5);FS=0.000;HRun=0;HaplotypeScore=0.0000;MQ=37.00;MQ0=0;QD=20.37 GT:AD:DP:GQ:PL 1/1:0,2:2:6:58,6,0 1/1:0,1:1:3.01:37,3,0 ./. ./.
chr10 126678092 . G A 89.08 . AC=1;AF=0.13;AN=8;BaseQRankSum=-3.120;CSQ=stop_gained|Caa/Taa|Q/*|ENSG00000175029|CTBP2|ENST00000531469|11/11||,stop_gained|Caa/Taa|Q/*|ENSG00000175029|CTBP2|ENST00000309035|9/9||,downstream_gene_variant|||ENSG00000019995|ZRANB1|ENST00000359653|||,stop_gained|Caa/Taa|Q/*|ENSG00000175029|CTBP2|ENST00000494626|11/11||,stop_gained|Caa/Taa|Q/*|ENSG00000175029|CTBP2|ENST00000337195|11/11||,stop_gained|Caa/Taa|Q/*|ENSG00000175029|CTBP2|ENST00000334808|9/9||,stop_gained|Caa/Taa|Q/*|ENSG00000175029|CTBP2|ENST00000411419|11/11||,downstream_gene_variant|||ENSG00000175029|CTBP2|ENST00000395705|||;DP=185;Dels=0.00;EFF=DOWNSTREAM(MODIFIER||||708|ZRANB1|protein_coding|CODING|ENST00000359653|),DOWNSTREAM(MODIFIER|||||CTBP2|processed_transcript|CODING|ENST00000395705|),STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q445*|445|CTBP2|protein_coding|CODING|ENST00000337195|),STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q445*|445|CTBP2|protein_coding|CODING|ENST00000411419|),STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q445*|445|CTBP2|protein_coding|CODING|ENST00000494626|),STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q445*|445|CTBP2|protein_coding|CODING|ENST00000531469|),STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q513*|513|CTBP2|protein_coding|CODING|ENST00000334808|),STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q985*|985|CTBP2|protein_coding|CODING|ENST00000309035|);FS=3.490;HRun=0;HaplotypeScore=3.3843;MQ=25.32;MQ0=0;MQRankSum=6.568;QD=2.02;ReadPosRankSum=-5.871 GT:AD:DP:GQ:PL 0/0:64,3:67:99:0,165,1505 0/0:11,1:12:7.31:0,7,240 0/0:52,10:62:54.97:0,55,1263 0/1:35,9:44:99:125,0,693
chr10 135210791 . T C 65.41 . AC=4;AF=0.50;AN=8;BaseQRankSum=2.054;CSQ=intron_variant|||ENSG00000148824||ENST00000317502|||,upstream_gene_variant|||ENSG00000148824||ENST00000492266|||,intron_variant&nc_transcript_variant|||ENSG00000148824||ENST00000460848|||,intron_variant|||ENSG00000254536|MTG1|ENST00000468317|||,intron_variant&nc_transcript_variant|||ENSG00000148824||ENST00000477902|||,intron_&nc_transcript_variant|||ENSG00000148824||ENST00000473735|||,intron_variant&nc_transcript_variant|||ENSG00000148824||ENST00000498790|||,intron_variant|||ENSG00000148824||ENST00000432508|||,intron_variant&nc_transcript_variant|||ENSG00000148824||ENST00000498334|||,intron_variant&nc_transcript_variant|||ENSG00000148824||ENST00000495014|||;DP=11;Dels=0.00;EFF=INTRON(MODIFIER||||283|MTG1|protein_coding|CODING|ENST00000432508|3),INTRON(MODIFIER||||334|MTG1|protein_coding|CODING|ENST00000317502|3),INTRON(MODIFIER||||339|MTG1|protein_coding|CODING|ENST00000468317|4),INTRON(MODIFIER|||||MTG1|processed_transcript|CODING|ENST00000460848|3),INTRON(MODIFIER|||||MTG1|processed_transcript|CODING|ENST00000473735|3),INTRON(MODIFIER|||||MTG1|processed_transcript|CODING|ENST00000477902|3),INTRON(MODIFIER|||||MTG1|processed_transcript|CODING|ENST00000495014|3),INTRON(MODIFIER|||||MTG1|processed_transcript|CODING|ENST00000498334|3),INTRON(MODIFIER|||||MTG1|processed_transcript|CODING|ENST00000498790|3),UPSTREAM(MODIFIER|||||MTG1|processed_transcript|CODING|ENST00000492266|);FS=0.000;HRun=0;HaplotypeScore=0.2489;MQ=35.12;MQ0=0;MQRankSum=0.248;QD=16.35;ReadPosRankSum=-1.001 GT:AD:DP:GQ:PL 0/0:4,0:4:9:0,9,84 1/1:0,3:3:6.02:74,6,0 1/1:0,1:1:3.01:37,3,0 0/0:3,0:3:9.02:0,9,100
chr13 48873835 . G A 58.95 . AC=4;AF=1.00;AN=4;CSQ=upstream_gene_variant|||ENSG00000139687|RB1|ENST00000467505|||,upstream_gene_variant|||ENSG00000139687|RB1|ENST00000525036|||,downstream_gene_variant|||ENSG00000231473|LINC00441|ENST00000436963|||,upstream_gene_variant|||ENSG00000139687|RB1|ENST00000267163|||,intron_variant&nc_transcript_variant|||ENSG00000231473|LINC00441|ENST00000433480|||;DP=3;Dels=0.00;EFF=DOWNSTREAM(MODIFIER|||||LINC00441|processed_transcript|NON_CODING|ENST00000436963|),INTRON(MODIFIER|||||LINC00441|processed_transcript|NON_CODING|ENST00000433480|2),UPSTREAM(MODIFIER||||928|RB1|protein_coding|CODING|ENST00000267163|),UPSTREAM(MODIFIER|||||RB1|nonsense_mediated_decay|CODING|ENST00000467505|),UPSTREAM(MODIFIER|||||RB1|retained_intron|CODING|ENST00000525036|);FS=0.000;HRun=1;HaplotypeScore=0.0000;MQ=37.00;MQ0=0;QD=19.65 GT:AD:DP:GQ:PL ./. ./. 1/1:0,2:2:6.01:62,6,0 1/1:0,1:1:3.01:31,3,0
chr20 36779424 . G A 128.76 . AC=1;AF=0.13;AN=8;BaseQRankSum=0.610;CSQ=non_coding_exon_variant&nc_transcript_variant|||ENSG00000198959|TGM2|ENST00000468262|4/10||,non_coding_exon_variant&nc_transcript_variant|||ENSG00000198959|TGM2|ENST00000485572|4/13||,non_coding_exon_variant&nc_transcript_variant|||ENSG00000198959|TGM2|ENST00000474777|4/6||,stop_gained|Cag/Tag|Q/*|ENSG00000198959|TGM2|ENST00000373403|5/7||,stop_gained|Cag/Tag|Q/*|ENSG00000198959|TGM2|ENST00000361475|4/13||,stop_gained|Cag/Tag|Q/*|ENSG00000198959|TGM2|ENST00000453095|5/5||,stop_gained|Cag/Tag|Q/*|ENSG00000198959|TGM2|ENST00000536701|3/12||,stop_gained|Cag/Tag|Q/*|ENSG00000198959|TGM2|ENST00000536724|3/12||;DP=196;Dels=0.00;EFF=EXON(MODIFIER|||||TGM2|processed_transcript|CODING|ENST00000485572|4),EXON(MODIFIER|||||TGM2|retained_intron|CODING|ENST00000468262|4),EXON(MODIFIER|||||TGM2|retained_intron|CODING|ENST00000474777|4),STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q157*|158|TGM2|protein_coding|CODING|ENST00000453095|),STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q157*|279|TGM2|protein_coding|CODING|ENST00000373403|),STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q157*|687|TGM2|protein_coding|CODING|ENST00000361475|),STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q76*|606|TGM2|protein_coding|CODING|ENST00000536701|),STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q97*|627|TGM2|protein_coding|CODING|ENST00000536724|);FS=1.447;HRun=0;HaplotypeScore=4.5749;MQ=36.22;MQ0=0;MQRankSum=-0.814;QD=3.90;ReadPosRankSum=-0.570 GT:AD:DP:GQ:PL 0/0:49,1:52:63.68:0,64,969 0/0:17,0:17:30.05:0,30,320 0/0:93,0:94:99:0,216,2384 0/1:24,9:33:99:165,0,505
chrX 17819377 . T C 7515.25 . AC=8;AF=1.00;AN=8;CSQ=downstream_gene_variant|||ENSG00000248906||ENST00000509491|||,missense_variant|Atg/Gtg|M/V|ENSG00000131831|RAI2|ENST00000360011|3/3|unknown(0)|tolerated(1),missense_variant|Atg/Gtg|M/V|ENSG00000131831|RAI2|ENST00000331511|3/3|unknown(0)|tolerated(1),missense_variant|Atg/Gtg|M/V|ENSG00000131831|RAI2|ENST00000415486|3/3|unknown(0)|tolerated(1),missense_variant|Atg/Gtg|M/V|ENSG00000131831|RAI2|ENST00000451717|2/2|unknown(0)|tolerated(1),missense_variant|Atg/Gtg|M/V|ENSG00000131831|RAI2|ENST00000545871|3/3|unknown(0)|tolerated(1);DP=319;Dels=0.00;EFF=DOWNSTREAM(MODIFIER|||||RP3-389A20.4|processed_transcript|NON_CODING|ENST00000509491|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M202V|480|RAI2|protein_coding|CODING|ENST00000415486|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M252V|530|RAI2|protein_coding|CODING|ENST00000331511|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M252V|530|RAI2|protein_coding|CODING|ENST00000360011|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M252V|530|RAI2|protein_coding|CODING|ENST00000451717|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atg/Gtg|M252V|530|RAI2|protein_coding|CODING|ENST00000545871|);FS=0.000;HRun=1;HaplotypeScore=7.7850;MQ=36.33;MQ0=0;QD=23.56 GT:AD:DP:GQ:PL 1/1:0,125:126:99:2343,237,0 1/1:0,26:26:78.14:837,78,0 1/1:0,90:92:99:2640,244,0 1/1:0,74:75:99:1695,171,0
```
<h:h4>Example 3</h:h4>
list the available SO:terms:
```
$ java -jar dist/vcffilterso.jar -S
SO:0001650 inframe_variant
SO:0001791 exon_variant
SO:0001792 non_coding_exon_variant
SO:0001593 minus_2_frameshift_variant
SO:0001594 plus_1_frameshift_variant
SO:0001595 plus_2_frameshift_variant
SO:0001596 transcript_secondary_structure_variant
SO:0001597 compensatory_transcript_secondary_structure_variant
SO:0001598 translational_product_structure_variant
SO:0001599 3D_polypeptide_structure_variant
(...)
```
## See also
* GroupByGene
* VCFPredictions
* http://www.sequenceontology.org/browser/obob.cgi
## History
* 2017 moved to jcommander
* END_DOC
*
*/
@Program(name="vcffilterso",keywords={"vcf","filter","sequenceontology","prediction","so"},
description="Filter a VCF file annotated with SNPEff or VEP with terms from Sequence-Ontology. Reasoning : Children of user's SO-terms will be also used.<")
public class VcfFilterSequenceOntology
extends Launcher
{
private static final Logger LOG = Logger.build(VcfFilterSequenceOntology.class).make();
@Parameter(names={"-i","--invert"},description="invert selection (if one of the user's term is found, do not accept the variant")
private boolean invert = false;
@Parameter(names={"-d","--noreasoning"},description="disable reasoning, don't use term's children.")
private boolean disableReasoning = false;
@Parameter(names={"-fi","--filterin"},description="Do not discard variant but add this FILTER its' prediction is found in the database")
private String filterIn = "";
@Parameter(names={"-fo","--filterout"},description="Do not discard variant but add this FILTER its' prediction is NOT found in the database")
private String filterOut = "";
@Parameter(names={"-r","--rmatt"},description="Do not remove the variant itself, just remove the mismatching Prediction: e.g: CSQ=OK,OK,NO,OK -> CSQ=OK,OK,OK")
private boolean removeUnusedAttribute = false;
@Parameter(names={"-R","--rmnoatt"},description="remove the variant if option -r was used and the is no more attribute")
private boolean removeIfNoMoreAttribute = false;
@Parameter(names={"-A","--acn"},description="add this SO:ACN.")
private List<String> userTermsAsString = new ArrayList<>();
@Parameter(names={"-f","--acnfile"},description="file of SO accession numbers")
private File userAcnFile = null;
@Parameter(names={"-S","--showacn"},description="list the available SO accession and exit.")
private boolean showList = false;
@Parameter(names={"-o","--out"},description="Output file or stdout")
private File outputFile = null;
@Parameter(names={"-owluri","--owluri"},description="If not empty, don't use the internal SO ontology but load a OWL description of the ontology. Tested with https://github.com/The-Sequence-Ontology/SO-Ontologies/raw/master/releases/so-xp.owl/so-xp-simple.owl")
private String owluri = "";
private SequenceOntologyTree sequenceOntologyTree = SequenceOntologyTree.createDefault();
/* all sequence terms */
private final Set<SequenceOntologyTree.Term> user_terms=new HashSet<SequenceOntologyTree.Term>();
private final Set<String> user_terms_strings=new HashSet<>();
public VcfFilterSequenceOntology()
{
}
@Override
protected int doVcfToVcf(final String inputName,final VcfIterator iter, final VariantContextWriter out) {
final VCFHeader header= iter.getHeader();
final VCFHeader header2= new VCFHeader(header);
final String termlist = String.join(", ",this.user_terms.stream().map(S->S.getAcn()+"("+S.getLabel()+")").collect(Collectors.toSet()));
if(!this.filterIn.isEmpty()) {
header2.addMetaDataLine(new VCFFilterHeaderLine(this.filterIn,
"Variant having SO terms:"+ termlist));
}
if(!this.filterOut.isEmpty()) {
header2.addMetaDataLine(new VCFFilterHeaderLine(this.filterOut,
"Variant non having SO terms :" + termlist));
}
this.user_terms_strings.clear();
this.user_terms_strings.addAll( this.user_terms.stream().
map(T->T.getLabel()).
collect(Collectors.toSet())
);
final VepPredictionParser vepParser =new VepPredictionParserFactory().header(header).get().sequenceOntologyTree(this.sequenceOntologyTree);
final SnpEffPredictionParser snpEffparser= new SnpEffPredictionParserFactory().header(header).get().sequenceOntologyTree(this.sequenceOntologyTree);
final MyPredictionParser myPredParser= new MyPredictionParser(header).sequenceOntologyTree(this.sequenceOntologyTree);
final AnnPredictionParser annPredParser= new AnnPredictionParserFactory().header(header).get().sequenceOntologyTree(this.sequenceOntologyTree);
out.writeHeader(header2);
while(iter.hasNext())
{
VariantContext ctx=iter.next();
boolean keep=false;
List<Object> snpEffPredStrings = null;
List<Object> vepPredStrings = null;
List<Object> myPredStrings = null;
List<Object> annPredStrings = null;
/* handle SNP EFF */
if(ctx.hasAttribute(snpEffparser.getTag())) {
snpEffPredStrings = new ArrayList<>(ctx.getAttributeAsList(snpEffparser.getTag()));
int x=0;
while(x<snpEffPredStrings.size()){
final Object predStr = snpEffPredStrings.get(x);
final SnpEffPredictionParser.SnpEffPrediction pred = snpEffparser.parseOnePrediction(predStr);
if(pred!=null && hasUserTem(pred.getSOTerms()))
{
keep=true;
++x;
}
else
{
snpEffPredStrings.remove(x);
}
}
}
/* handle VEP */
if(ctx.hasAttribute(vepParser.getTag()) && (this.removeUnusedAttribute || !keep)) {
vepPredStrings = new ArrayList<>(ctx.getAttributeAsList(vepParser.getTag()));
int x=0;
while(x<vepPredStrings.size()){
final Object predStr = vepPredStrings.get(x);
final VepPredictionParser.VepPrediction pred = vepParser.parseOnePrediction(ctx, predStr);
if(pred!=null && hasUserTemLabel(pred.getSOTermsStrings()))
{
keep=true;
++x;
}
else
{
vepPredStrings.remove(x);
}
}
}
/* handle MyPredictionParser */
if(ctx.hasAttribute(myPredParser.getTag()) && (this.removeUnusedAttribute || !keep)) {
myPredStrings = new ArrayList<>(ctx.getAttributeAsList(myPredParser.getTag()));
int x=0;
while(x<myPredStrings.size()){
final Object predStr = myPredStrings.get(x);
final MyPredictionParser.MyPrediction pred = myPredParser.parseOnePrediction(predStr);
if(pred!=null && hasUserTem(pred.getSOTerms()))
{
keep=true;
++x;
}
else
{
myPredStrings.remove(x);
}
}
}
/* handle ANN */
if(ctx.hasAttribute(annPredParser.getTag()) && (this.removeUnusedAttribute || !keep)) {
annPredStrings = new ArrayList<>(ctx.getAttributeAsList(annPredParser.getTag()));
int x=0;
while(x<annPredStrings.size()){
final Object predStr = annPredStrings.get(x);
final AnnPredictionParser.AnnPrediction pred = annPredParser.parseOnePrediction(predStr);
if(pred!=null && hasUserTemLabel(pred.getSOTermsStrings()))
{
keep=true;
++x;
}
else
{
annPredStrings.remove(x);
}
}
}
if(this.removeUnusedAttribute)
{
final VariantContextBuilder vcb = new VariantContextBuilder(ctx);
int count=0;
if(snpEffPredStrings!=null) {
vcb.rmAttribute(snpEffparser.getTag());
vcb.attribute(snpEffparser.getTag(), snpEffPredStrings);
count += snpEffPredStrings.size();
}
if(vepPredStrings!=null) {
vcb.rmAttribute(vepParser.getTag());
vcb.attribute(vepParser.getTag(), vepPredStrings);
count += vepPredStrings.size();
}
if(myPredStrings!=null) {
vcb.rmAttribute(myPredParser.getTag());
vcb.attribute(myPredParser.getTag(), myPredStrings);
count += myPredStrings.size();
}
if(annPredStrings!=null) {
vcb.rmAttribute(annPredParser.getTag());
vcb.attribute(annPredParser.getTag(), annPredStrings);
count += annPredStrings.size();
}
if( count == 0 && this.removeIfNoMoreAttribute)
{
addVariant(out,vcb.make(),false);
}
else
{
addVariant(out,vcb.make(),true);
}
}
else
{
addVariant(out,ctx,keep);
}
}
return 0;
}
private void addVariant(final VariantContextWriter w,final VariantContext ctx,boolean keep)
{
if(this.invert) keep=!keep;
if(!this.filterIn.isEmpty())
{
if(keep){
final VariantContextBuilder vcb=new VariantContextBuilder(ctx);
vcb.filter(this.filterIn);
w.add(vcb.make());
}
else if( !ctx.filtersWereApplied()) {
final VariantContextBuilder vcb=new VariantContextBuilder(ctx);
vcb.passFilters();
w.add(vcb.make());
}
else
{
w.add(ctx);
}
}
else if(!this.filterOut.isEmpty()) {
if(keep && !ctx.filtersWereApplied()) {
final VariantContextBuilder vcb=new VariantContextBuilder(ctx);
vcb.passFilters();
w.add(vcb.make());
}
else if(keep){
w.add(ctx);
}
else
{
final VariantContextBuilder vcb=new VariantContextBuilder(ctx);
vcb.filter(this.filterOut);
w.add(vcb.make());
}
}
else
{
if(keep) {
w.add(ctx);
} else
{
/* don't print */
}
}
}
private boolean hasUserTem(final Set<SequenceOntologyTree.Term> ctxTerms)
{
return ctxTerms.
stream().
filter(S->user_terms.contains(S)).findAny().isPresent();
}
private boolean hasUserTemLabel(final Collection<String> ctxTerms)
{
return ctxTerms.
stream().
filter(S->user_terms_strings.contains(S)).findAny().isPresent();
}
private void parseAccessionsFile(final File f) throws IOException
{
final BufferedReader in=IOUtils.openFileForBufferedReading(f);
String line;
while((line=in.readLine())!=null)
{
if(line.startsWith("#")) continue;
line=line.trim();
if(line.trim().isEmpty()) continue;
this.userTermsAsString.add(line);
}
in.close();
}
@Override
public int doWork(final List<String> args) {
try {
if( !(this.owluri==null || this.owluri.trim().isEmpty()) ) {
LOG.info("loading so tree from "+this.owluri);
this.sequenceOntologyTree = SequenceOntologyTree.fromUri(this.owluri.trim());
LOG.info("Done loading SO.");
}
if(this.showList)
{
final PrintWriter pw=super.openFileOrStdoutAsPrintWriter(this.outputFile);
for(SequenceOntologyTree.Term t:this.sequenceOntologyTree.getTerms())
{
pw.println(t.getAcn()+"\t"+t.getLabel());
}
pw.close();
return 0;
}
final boolean reasoning = !this.disableReasoning;
if(this.userAcnFile!=null)
{
this.parseAccessionsFile(this.userAcnFile);
}
this.userTermsAsString.stream().
map(S->S.trim()).
filter(S->!S.isEmpty()).
forEach(acn->{
final SequenceOntologyTree.Term t= this.sequenceOntologyTree.getTermByAcn(acn);
if(t==null)
{
throw new JvarkitException.UserError("Unknown SO:Accession \""+acn+"\"");
}
this.user_terms.add(t);
if(reasoning) this.user_terms.addAll(t.getAllDescendants());
});
if(this.user_terms.isEmpty())
{
LOG.warn("No SO: term found ");
}
LOG.info("Will be using :"+this.user_terms.stream().
map(T->T.getAcn()+"("+T.getLabel()+")").
collect(Collectors.joining(" ")));
this.userTermsAsString.clear();//we don't need this anymore
if(this.invert && this.removeUnusedAttribute) {
LOG.error("Option invert cannot be used when Option removeUnusedAttribute is set");
return -1;
}
if(!this.filterIn.isEmpty() && !this.filterOut.isEmpty()) {
LOG.error("Option filterIn && filterOut both defined.");
return -1;
}
if((this.invert) && (!this.filterIn.isEmpty() || !this.filterOut.isEmpty())) {
LOG.error("Option invert cannot be used when Option filterIn or filterOut is defined.");
return -1;
}
return doVcfToVcf(args, this.outputFile);
}
catch(final Exception err) {
LOG.error(err);
return -1;
}
finally
{
}
}
public static void main(String[] args)
{
new VcfFilterSequenceOntology().instanceMainWithExit(args);
}
}