a95486084d48d3739b6d995a11f2cea55754f10c jeltje.van.baren Fri Apr 18 12:16:18 2025 -0700 better labeling and searching of Yale pseudogene track diff --git src/hg/makeDb/doc/hg38/pseudogenes.txt src/hg/makeDb/doc/hg38/pseudogenes.txt index 1ec5da3c10b..e75604ea968 100755 --- src/hg/makeDb/doc/hg38/pseudogenes.txt +++ src/hg/makeDb/doc/hg38/pseudogenes.txt @@ -25,94 +25,95 @@ ./pseudoPipeToBed.py --genes all.ids --gtf uniq.gtf --bed pgene.bed # change the chromosome IDs (they need to match the parents) bigBedToBed /gbdb/hg38/hg38.chromAlias.bb chromAlias.bed tawk '{print $6, $1}' chromAlias.bed > sub.list subColumn 1 pgene.bed sub.list pgene2.bed bedSort pgene2.bed pgene.bed ########## PARENT TRACK ###################### # Create a parent track and add parent info to the children ### V37 -# we only need the chrom coords, not the blocks -zcat /hive/data/genomes/hg38/bed/gencodeV37/build/gencodeV37.bed.gz | cut -f1-6 > v37.tsv - -# these have ENST IDs but not gene IDs -# replace with gene IDs (note that this creates duplicate IDs in the file) -paste <(cut -f3 all.ids) <(cut -f1 all.ids | cut -f1 -d'.') > sub.me -subColumn -miss=idMiss.txt 4 v37.tsv sub.me v37.sub -#grep -c ENST v37.sub # 0 +zcat /hive/data/genomes/hg38/bed/gencodeV37/build/gencodeV37.bed.gz > v37.bed ### V38 bigBedToBed /hive/data/genomes/hg38/bed/gencodeV38/build/hg38.gencodeV38.bb V38.bed -subColumn -miss=idMiss.txt 4 <(cut -f1-6 V38.bed) sub.me v38.sub -#grep -c ENST v38.sub # 0 # we really only want v37 genes if they are not in v38 -selectById -not 4 v38.sub 4 v37.sub > addMe +selectById -not 4 V38.bed 4 v37.bed > addMe # sort by gene ID, then chr -cat v38.sub addMe | sort -k4 -k1 > annot.bed +cat V38.bed addMe | sort -k4 -k1 | cut -f1-12> annot.bed ./pseudoPipeParents.py --pgenebed pgene.bed --annotbed annot.bed --pgeneout pseudopipePgenes.bed --parentout parents.bed ### convert to bigbed ### cat << '_EOF_' > pseudoPipePgenes.as table yale_pseudogenes -"Bed 12+6 file with pseudogenes and their (gene, transcript, and protein) parents." +"Bed 12+11 file with pseudogenes and their (gene, transcript, and protein) parents." ( string chrom; "Chromosome (or contig, scaffold, etc.)" uint chromStart; "Start position in chromosome" uint chromEnd; "End position in chromosome" string name; "Name of item" uint score; "Score from 0-1000" char[1] strand; "+ or -" uint thickStart; "Start of where display should be thick (start codon)" uint thickEnd; "End of where display should be thick (stop codon)" uint reserved; "Used as itemRgb as of 2004-11-22" int blockCount; "Number of blocks" int[blockCount] blockSizes; "Comma separated list of block sizes" int[blockCount] chromStarts; "Start positions relative to chromStart" - string hugo; "Pseudogene of" - string pgeneType; "pseudogene, processed_pseudogene, unprocessed_pseudogene" - string ppgene; "Pseudopipe pseudogene ID" - string gene; "Ensembl pseudogene ID" - string geneParent; "Ensembl gene parent ID (url)" - string proteinParent; "Ensembl protein parent ID" + string pgenehugo; "Pseudogene HUGO ID" + string parenthugo; "Parent pseudogene HUGO ID" + string ppgene; "Pseudopipe pseudogene gene ID" + string pptx; "Pseudopipe pseudogene transcript ID" + string pgeneType; "Pseudogene type" + string pensgene; "Ensembl pseudogene gene ID" + string penstx; "Ensembl pseudogene transcript ID" + string ensgene; "Ensembl parent gene ID" + string _enstx; "Ensembl parent transcript ID" + string ensprot; "Ensembl parent protein ID" + string enstxurl; "Ensembl parent transcript ID (url)" ) _EOF_ -bedToBigBed -type=bed12+8 -tab -as=pseudoPipePgenes.as -extraIndex=hugo,name,ppgene pseudopipePgenes.bed /hive/data/genomes/hg38/chrom.sizes pseudoPipePgenes.bb +bedToBigBed -type=bed12+10 -tab -as=pseudoPipePgenes.as -extraIndex=pgenehugo,parenthugo,name,ppgene,pptx,pensgene,penstx,ensgene,_enstx,ensprot pseudopipePgenes.bed /hive/data/genomes/hg38/chrom.sizes pseudoPipePgenes.bb + # trix index (make search case insensitive) for hugo and ENSG parent IDs -cut -f4,14,18 pseudopipePgenes.bed > name.table +cut -f4,13-16,18-22 pseudopipePgenes.bed > name.table ixIxx name.table pseudoPipePgenes.ix pseudoPipePgenes.ixx cat << '_EOF_' > pseudoPipeParents.as table yale_parents -"Bed 9+2 file with parents and and their pseudogenes." +"Bed 12+3 file with parents and and their pseudogenes." ( string chrom; "Chromosome (or contig, scaffold, etc.)" uint chromStart; "Start position in chromosome" uint chromEnd; "End position in chromosome" string name; "Name of item" uint score; "Score from 0-1000" char[1] strand; "+ or -" uint thickStart; "Start of where display should be thick (start codon)" uint thickEnd; "End of where display should be thick (stop codon)" uint reserved; "Used as itemRgb as of 2004-11-22" - string hugo; "Gene symbol" - string url; "Link to pseudogene" + int blockCount; "Number of blocks" + int[blockCount] blockSizes; "Comma separated list of block sizes" + int[blockCount] chromStarts; "Start positions relative to chromStart" + string hugo; "Gene ID" + string geneType; "Gene type" + lstring url; "Link to pseudogene" ) _EOF_ # sort so that ENSG comes before PGO Ids, putting the parent at the top sort -k1,1 -k2,2n -k4 parents.bed > pseudopipeParents.bed -bedToBigBed -type=bed9+2 -tab -as=pseudoPipeParents.as pseudopipeParents.bed /hive/data/genomes/hg38/chrom.sizes pseudoPipeParents.bb +bedToBigBed -type=bed12+3 -tab -as=pseudoPipeParents.as pseudopipeParents.bed /hive/data/genomes/hg38/chrom.sizes pseudoPipeParents.bb cut -f4,10 pseudopipeParents.bed > name.table ixIxx name.table pseudoPipeParents.ix pseudoPipeParents.ixx rm addMe v37.tsv v38.sub V38.bed v37.sub sub.me sub.list idMiss.txt rm *.bed rm name.table uniq.gtf all.ids