ebd704b803fed9f990e2c8aeda1338a7054f8316 braney Wed Feb 22 17:43:49 2012 -0800 more moving things around #6943 diff --git src/utils/omim/buildOmimTracks.csh src/utils/omim/buildOmimTracks.csh deleted file mode 100755 index 5c4a34c..0000000 --- src/utils/omim/buildOmimTracks.csh +++ /dev/null @@ -1,167 +0,0 @@ -#!/bin/tcsh -# BUILD $1 OMIM RELATED TRACKS - -cat genemap|sed -e 's/|/\t/g' > genemap.tab - -hgLoadSqlTab -warn $1 omimGeneMap ~/kent/src/hg/lib/omimGeneMap.sql genemap.tab - -# Load mim2gene table - -fgrep -v "gene/phenotype" mim2gene.txt > j.tmp.1 -fgrep "gene/phenotype" mim2gene.txt > j.tmp.2 - -cut -f 2 j.tmp.2|sed -e 's/\//\t/' >j.tmp - -cut -f 1 j.tmp.2 >j.1 - -cut -f 1 j.tmp >j.g -cut -f 2 j.tmp >j.p - -cut -f 3-5 j.tmp.2 >j.345 - -paste j.1 j.g j.345 >jj.g -paste j.1 j.p j.345 >jj.p - -cat j.tmp.1 jj.g jj.p >mim2gene.updated.txt - -rm j.* jj.* - - -cut -f 1 mim2gene.updated.txt >j1 -cut -f 2 mim2gene.updated.txt >j2 -cut -f 3 mim2gene.updated.txt >j3 - -paste j1 j3 j2 >mim2gene.tab - -hgsql $1 -e 'drop table mim2gene' -hgsql $1 < ~/kent/src/hg/lib/mim2gene.sql - -hgsql $1 -e 'load data local infile "mim2gene.tab" into table mim2gene ignore 1 lines' - - -hgsql $1 -e 'drop table omim2gene' -hgsql $1 < ~/kent/src/hg/lib/omim2gene.sql - -hgsql $1 -e 'load data local infile "mim2gene.updated.txt" into table omim2gene ignore 1 lines' - -# build omimGeneSymbol table - -doOmimGeneSymbols $1 j.out -cat j.out |sort -u >omimGeneSymbol.tab - -hgLoadSqlTab -warn $1 omimGeneSymbol ~/kent/src/hg/lib/omimGeneSymbol.sql omimGeneSymbol.tab - -perl ./parseGeneMap.pl --gene-map-file=genemap >omimPhenotype.tab - -hgLoadSqlTab -warn $1 omimPhenotype ~/kent/src/hg/lib/omimPhenotype.sql omimPhenotype.tab - -hgsql $1 -e 'update omimPhenotype set omimPhenoMapKey = -1 where omimPhenoMapKey=0' -hgsql $1 -e 'update omimPhenotype set phenotypeId = -1 where phenotypeId=0' - -doOmimGene2 $1 j.tmp -cat j.tmp |sort -u > omimGene2.tab - -hgLoadBed $1 omimGene2 omimGene2.tab - -rm j.tmp -############################################################## -# build the omimAvSnp track - -mkdir -p av -cd av - -# get the mimAV.txt data file from OMIM - -cp ../mimAV.txt . -p - -cut -f 1 mimAV.txt >j1 -cut -f 2 mimAV.txt >j2 -cut -f 3 mimAV.txt >j3 -cut -f 4 mimAV.txt >j4 -cut -f 5 mimAV.txt >j5 - -cat j1 |sed -e 's/\./\t/' >j1.2 - -cat j4 |sed -e 's/,/\t/' >j4-2 -cut -f 1 j4-2 >j4.1 -cut -f 2 j4-2 >j4.2 - -paste j1 j1.2 j3 j4 j4.1 j4.2 j5 j2 >omimAv.tab - -hgsql $1 -e 'drop table omimAv' -hgsql $1 < ~/src/hg/lib/omimAv.sql -hgsql $1 -e 'load data local infile "omimAv.tab" into table omimAv ignore 1 lines' -hgsql $1 -e 'update omimAv set repl2 = rtrim(ltrim(repl2))' - -doOmimAv $1 omimAvRepl.tab j.err - -hgsql $1 -e "drop table omimAvRepl" -hgsql $1 < ~/kent/src/hg/lib/omimAvRepl.sql -hgsql $1 -e 'load data local infile "omimAvRepl.tab" into table omimAvRepl' - -rm j1.2 j1 j2 j3 j4 j4-2 j4.1 j4.2 j5 - -if ($1 == "hg18") then - hgsql $1 -N -e 'select chrom, chromStart, chromEnd, avId from omimAvRepl r, snp130 s where s.name = dbSnpId order by avId' |sort -u > omimAvSnp.tab -else - hgsql $1 -N -e 'select chrom, chromStart, chromEnd, avId from omimAvRepl r, snp132 s where s.name = dbSnpId order by avId' |sort -u > omimAvSnp.tab -endif - -hgLoadBed -allowStartEqualEnd $1 omimAvSnp omimAvSnp.tab -cd .. - -############################################################## -echo build omimLocation ... - -mkdir -p location -cd location - -doOmimLocation $1 omimLocation.bed j.err - -hgLoadBed $1 omimLocation omimLocation.bed - -# Remove all gene entries in omimGene2 from omimLocation table - -hgsql $1 -N -e \ -'delete from omimLocation where name in (select name from omimGene2) ' - -# Per OMIM request, delete all the gray entries in omimLocation table. - -mkdir -p cleanUpOmimLocation -cd cleanUpOmimLocation - -echo cleaning omimLocation ... - -hgsql $1 -N -e \ -'select distinct name from omimLocation' |sort -u >j.all - -hgsql $1 -N -e \ -'select distinct name from omimLocation, omimPhenotype where name=omimId and omimPhenoMapKey=1' >j.1 -hgsql $1 -N -e \ -'select distinct name from omimLocation, omimPhenotype where name=omimId and omimPhenoMapKey=2' >j.2 -hgsql $1 -N -e \ -'select distinct name from omimLocation, omimPhenotype where name=omimId and omimPhenoMapKey=3' >j.3 -hgsql $1 -N -e \ -'select distinct name from omimLocation, omimPhenotype where name=omimId and omimPhenoMapKey=4' >j.4 - -cat j.1 j.2 j.3 j.4 |sort -u >j.1234 - -diff j.all j.1234 |grep "<" |sed -e "s/</do1 ${1}/" >doall - -#cat doall - -cat << '_EOF_' > do1 -hgsql $1 -e "delete from omimLocation where name='${2}'" -'_EOF_' - -#sleep 3 -#echo after sleep - -chmod +x do1 -chmod +x doall -./doall - -############################################################## - -# remember to check in new mim2gene.sql -