Created
April 4, 2024 10:59
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Tool to Identify Gene, Regulatory Role, and Function at Integration Sites https://www.biostars.org/p/9591769/
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| BEGIN { | |
| FS="\t"; | |
| } | |
| ($3=="gene") { | |
| gene_id=""; | |
| gene_name="" | |
| gene_biotype="" | |
| N=split($9,a,/[ ]*[;][ ]*/); | |
| for(i=1;i<=N;++i) { | |
| N2 = split(a[i],b,/[ ]/); | |
| K = b[1]; | |
| V=b[2]; | |
| gsub(/"/,"",V); | |
| if(K=="gene_id") gene_id=V; | |
| else if(K=="gene_name") gene_name=V; | |
| else if(K=="gene_biotype") gene_biotype=V; | |
| } | |
| if(gene_id=="") next; | |
| printf("<bio:Gene rdf:about=\"%s\">\n",gene_id); | |
| printf("\t<bio:gene_id>%s</bio:gene_id>\n",gene_id); | |
| if(gene_name!="") printf("\t<bio:gene_name>%s</bio:gene_name>\n",gene_name); | |
| if(gene_biotype!="") printf("\t<bio:gene_biotype>%s</bio:gene_biotype>\n",gene_biotype); | |
| printf("\t<bio:location>\n"); | |
| printf("\t\t<bio:Location>\n"); | |
| printf("\t\t\t<bio:build>%s</bio:build>\n",BUILD); | |
| printf("\t\t\t<bio:chrom>%s</bio:chrom>\n",$1); | |
| printf("\t\t\t<bio:start rdf:datatype=\"http://www.w3.org/2001/XMLSchema#int\">%s</bio:start>\n",$4); | |
| printf("\t\t\t<bio:end rdf:datatype=\"http://www.w3.org/2001/XMLSchema#int\">%s</bio:end>\n",$5); | |
| printf("\t\t</bio:Location>\n"); | |
| printf("\t</bio:location>\n"); | |
| printf("</bio:Gene>\n"); | |
| } |
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| SHELL=/bin/bash | |
| OUTDIR=TMP | |
| BUILD=GRCh38 | |
| all: $(OUTDIR)/database.rdf query.01.sparql | |
| /path/to/pache-jena-4.8.0/bin/arq --data=$< --query=query.01.sparql | |
| $(OUTDIR)/database.rdf: $(OUTDIR)/go.rdf $(OUTDIR)/gtf.rdf | |
| mkdir -p $(dir $@) | |
| echo '<?xml version="1.0" encoding="UTF-8"?><rdf:RDF xmlns:bio="https://www.biostars.org/#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xml:base="https://www.biostars.org/">' > $@ | |
| cat $^ >> $@ | |
| echo "</rdf:RDF>" >> $@ | |
| $(OUTDIR)/go.rdf: | |
| mkdir -p $(dir $@) | |
| wget -O - "https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz" | gunzip -c |\ | |
| awk -F '\t' '$$1==9606' | cut -f 2,3,6 | sort -T $(dir $@) -t $$'\t' -k1,1 > $(addsuffix .tmp1,$@) | |
| wget -O - "https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2ensembl.gz" | gunzip -c |\ | |
| awk -F '\t' '$$1==9606' | cut -f 2,3 | sort -T $(dir $@) -t $$'\t' -k1,1 > $(addsuffix .tmp2,$@) | |
| join -t $$'\t' -1 1 -2 1 $(addsuffix .tmp1,$@) $(addsuffix .tmp2,$@) > $(addsuffix .tmp3,$@) | |
| cut -f 2,3 $(addsuffix .tmp3,$@) | sort -T $(dir $@) | uniq |\ | |
| awk -F '\t' '{GO=$$1;gsub(/:/,"_",GO); printf("<bio:Term rdf:about=\"%s\"><bio:go_id>%s</bio:go_id><rdfs:label>%s</rdfs:label></bio:Term>\n",GO,$$1,$$2);}' >> $@ | |
| cut -f 2,4 $(addsuffix .tmp3,$@) | awk -F '\t' '{GO=$$1;gsub(/:/,"_",GO); printf("<rdf:Description rdf:about=\"%s\"><bio:has_go_term rdf:resource=\"%s\"/></rdf:Description>\n",$$2,GO);}' >> $@ | |
| rm $(addsuffix .tmp1,$@) $(addsuffix .tmp2,$@) $(addsuffix .tmp3,$@) | |
| $(OUTDIR)/gtf.rdf : gtf2rdf.awk | |
| mkdir -p $(dir $@) | |
| wget -O - "https://ftp.ensembl.org/pub/release-111/gtf/homo_sapiens/Homo_sapiens.$(BUILD).111.chr.gtf.gz" | gunzip -c |\ | |
| awk '($$1=="1")' |\ | |
| awk -vBUILD=$(BUILD) -f gtf2rdf.awk > $@ |
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| PREFIX bio: <https://www.biostars.org/#> | |
| PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#> | |
| PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#> | |
| SELECT | |
| ?build | |
| ?chrom | |
| ?start | |
| ?end | |
| ?gene_id | |
| ?gene_name | |
| ?gene_biotype | |
| ?go_id | |
| ?go_label | |
| WHERE { | |
| ?gene bio:gene_name ?gene_name . | |
| ?gene bio:gene_biotype ?gene_biotype . | |
| ?gene bio:gene_id ?gene_id . | |
| ?gene bio:location ?loc . | |
| ?loc a bio:Location . | |
| ?loc bio:build ?build . | |
| ?loc bio:chrom ?chrom . | |
| ?loc bio:start ?start . | |
| ?loc bio:end ?end . | |
| OPTIONAL { | |
| ?gene bio:has_go_term ?go . | |
| ?go bio:go_id ?go_id . | |
| ?go rdfs:label ?go_label . | |
| } | |
| FILTER( ?start <= 20746689 ) . | |
| FILTER( ?end >= 20746689 ) . | |
| FILTER( ?chrom = "1" ) . | |
| } |
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| ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | |
| | build | chrom | start | end | gene_id | gene_name | gene_biotype | go_id | go_label | | |
| ================================================================================================================================================================================================================================================ | |
| | "GRCh38" | "1" | "20740266"^^<http://www.w3.org/2001/XMLSchema#int> | "20787323"^^<http://www.w3.org/2001/XMLSchema#int> | "ENSG00000127483" | "HP1BP3" | "protein_coding" | "GO:0006334" | "nucleosome assembly" | | |
| | "GRCh38" | "1" | "20740266"^^<http://www.w3.org/2001/XMLSchema#int> | "20787323"^^<http://www.w3.org/2001/XMLSchema#int> | "ENSG00000127483" | "HP1BP3" | "protein_coding" | "GO:0000786" | "nucleosome" | | |
| | "GRCh38" | "1" | "20740266"^^<http://www.w3.org/2001/XMLSchema#int> | "20787323"^^<http://www.w3.org/2001/XMLSchema#int> | "ENSG00000127483" | "HP1BP3" | "protein_coding" | "GO:0005634" | "nucleus" | | |
| | "GRCh38" | "1" | "20740266"^^<http://www.w3.org/2001/XMLSchema#int> | "20787323"^^<http://www.w3.org/2001/XMLSchema#int> | "ENSG00000127483" | "HP1BP3" | "protein_coding" | "GO:0070828" | "heterochromatin organization" | | |
| | "GRCh38" | "1" | "20740266"^^<http://www.w3.org/2001/XMLSchema#int> | "20787323"^^<http://www.w3.org/2001/XMLSchema#int> | "ENSG00000127483" | "HP1BP3" | "protein_coding" | "GO:0031491" | "nucleosome binding" | | |
| | "GRCh38" | "1" | "20740266"^^<http://www.w3.org/2001/XMLSchema#int> | "20787323"^^<http://www.w3.org/2001/XMLSchema#int> | "ENSG00000127483" | "HP1BP3" | "protein_coding" | "GO:0006355" | "regulation of DNA-templated transcription" | | |
| | "GRCh38" | "1" | "20740266"^^<http://www.w3.org/2001/XMLSchema#int> | "20787323"^^<http://www.w3.org/2001/XMLSchema#int> | "ENSG00000127483" | "HP1BP3" | "protein_coding" | "GO:0003677" | "DNA binding" | | |
| | "GRCh38" | "1" | "20740266"^^<http://www.w3.org/2001/XMLSchema#int> | "20787323"^^<http://www.w3.org/2001/XMLSchema#int> | "ENSG00000127483" | "HP1BP3" | "protein_coding" | "GO:0005694" | "chromosome" | | |
| | "GRCh38" | "1" | "20740266"^^<http://www.w3.org/2001/XMLSchema#int> | "20787323"^^<http://www.w3.org/2001/XMLSchema#int> | "ENSG00000127483" | "HP1BP3" | "protein_coding" | "GO:0016607" | "nuclear speck" | | |
| | "GRCh38" | "1" | "20740266"^^<http://www.w3.org/2001/XMLSchema#int> | "20787323"^^<http://www.w3.org/2001/XMLSchema#int> | "ENSG00000127483" | "HP1BP3" | "protein_coding" | "GO:0042127" | "regulation of cell population proliferation" | | |
| | "GRCh38" | "1" | "20740266"^^<http://www.w3.org/2001/XMLSchema#int> | "20787323"^^<http://www.w3.org/2001/XMLSchema#int> | "ENSG00000127483" | "HP1BP3" | "protein_coding" | "GO:0005515" | "protein binding" | | |
| | "GRCh38" | "1" | "20740266"^^<http://www.w3.org/2001/XMLSchema#int> | "20787323"^^<http://www.w3.org/2001/XMLSchema#int> | "ENSG00000127483" | "HP1BP3" | "protein_coding" | "GO:0097298" | "regulation of nucleus size" | | |
| | "GRCh38" | "1" | "20740266"^^<http://www.w3.org/2001/XMLSchema#int> | "20787323"^^<http://www.w3.org/2001/XMLSchema#int> | "ENSG00000127483" | "HP1BP3" | "protein_coding" | "GO:0071456" | "cellular response to hypoxia" | | |
| ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
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