ecfd1eef6885909797fafb4c5da8f934971de265 kate Thu May 30 07:47:34 2019 -0700 Remove chrEBV from tables. refs #23243 diff --git src/hg/makeDb/doc/encode3/tfbs.txt src/hg/makeDb/doc/encode3/tfbs.txt index 1c42f25..e5becbc 100644 --- src/hg/makeDb/doc/encode3/tfbs.txt +++ src/hg/makeDb/doc/encode3/tfbs.txt @@ -329,30 +329,31 @@ hgsql hg38 -e "alter table encode3RegTfbsCluster rename to encRegTfbsClustered" hgsql hg38 -e "alter table encode3RegTfbsClusterInput rename to encRegTfbsClusteredInputs" hgsql hg38 -e "alter table encode3RegTfbsExp rename to encRegTfbsClusteredSources" ################ # Load per-factor tables (needed for clusters track details # Consider also creating a track for these (composite with 1200 subtracks) cat > scorePeaks.csh << 'EOF' set db = $1 set f = $2 set t = $f:r:r set table = encode3TfbsPk$t echo $table +# next time grep out chrEBV zcat $f > $table.bed bedScore -col=7 -verbose=2 -method=reg -uniform $f $table.scored.bed hgLoadBed -noNameIx -trimSqlTable \ -sqlTable=$HOME/kent/src/hg/lib/encode/narrowPeak.sql -renameSqlTable \ -as=$HOME/kent/src/hg/lib/encode/narrowPeak.as $db $table $table.scored.bed gzip -c $table.scored.bed > ../scoredPeaks/$table.bed.gz rm $table.bed $table.scored.bed end 'EOF' cd hg19 mkdir scoredPeaks cd peaks awk '{print $1}' ../fileCellAbTarget.tab | sed 's/peaks\///' | \ @@ -374,30 +375,34 @@ # Fix up subGroup members w/ punctuation and initial numbers: # Peyer's_patch -> Peyers_patch # NT2/D1 -> NT2_D1 # 22Rv1 -> X22Rv1 # MM.1S -> MM_1S # rename tables (encode3Tfbs -> encTfChipPk) hgsql hg19 -e 'show tables like "encode3TfbsPk%"' > tables.old.txt sed -e 's/^/alter table /' -e 's/$/ rename to /' tables.old.txt > rename.1.sql sed -e 's/encode3TfbsPk/encTfChipPk/' tables.old.txt | paste rename.1.sql - | \ sed 's/$/;/' > rename.sql hgsql hg19 < rename.sql +# drop chrEBV from tables +# edit/copy rename.sql to dropEbv.csh: delete from <table> where chrom='chrEBV' +hgsql hg19 < dropEbv.sql + # add colors to tier1-3 cell experiments (using ENCODE 2 color conventions) # # GM12878 color 153,38,0 # H1-hESC color 0,107,27 # K562 color 46,0,184 # HeLa-S3 color 0,119,158 # HepG2 color 189,0,157 # HUVEC color 224,75,0 raToLines encode3.ra encode3.lines sed -e '/GM12878/s/$/| color 153,38,0/' \ -e '/H1-hESC/s/$/| color 0,107,27/' \ -e '/K562/s/$/| color 46,0,184/' \ -e '/HeLa-S3/s/$/| color 0,119,158/' \ -e '/HepG2/s/$/| color 189,0,157/' \ @@ -444,30 +449,34 @@ # Fix up subGroup members w/ punctuation and initial numbers: # Peyer's_patch -> Peyers_patch # NT2/D1 -> NT2_D1 # 22Rv1 -> X22Rv1 # MM.1S -> MM_1S # rename tables (encode3Tfbs -> encTfChipPk) hgsql hg38 -e 'show tables like "encode3TfbsPk%"' > tables.old.txt sed -e 's/^/alter table /' -e 's/$/ rename to /' tables.old.txt > rename.1.sql sed -e 's/encode3TfbsPk/encTfChipPk/' tables.old.txt | paste rename.1.sql - | \ sed 's/$/;/' > rename.sql hgsql hg38 < rename.sql +# drop chrEBV from tables +# edit/copy rename.sql to dropEbv.csh: delete from <table> where chrom='chrEBV' +hgsql hg38 < dropEbv.sql + # add colors, using DNase similarity track raToLines encode3.ra encode3.lines # edit to leave only subtracks # generate edit script from DNase similarity .ra file cd ~/kent/src/hg/makeDb/trackDb/human/hg38 csh addColors.csh encode3.lines > encode3.color.lines linesToRa encode3.color.lines encode3.color.ra # missed a few (punctuation diffs, etc.) csh addColors2.csh encode3.color.lines encode3.color2.lines linesToRa encode3.color2.lines encode3.color.ra # merge in to encode3.ra