5e93998ad4e2934a13e49d2fe9c64c8251795fac
braney
  Wed Nov 16 12:19:22 2022 -0800
otto-mate the ClinVar Submissions track

diff --git src/hg/utils/otto/clinvar/clinvarSubLolly src/hg/utils/otto/clinvar/clinvarSubLolly
index a31eef6..dfe96a1 100755
--- src/hg/utils/otto/clinvar/clinvarSubLolly
+++ src/hg/utils/otto/clinvar/clinvarSubLolly
@@ -1,20 +1,42 @@
+#!/bin/bash -e
+maxDiff=$2
+dbs="hg19 hg38"
 
-bigBedToBed /gbdb/hg38/bbi/clinvar/clinvarMain.bb stdout | tawk '{print $40, $1,$2,$2+1,$4}' | sort  -S 40g > sort.main.bed
-hgsql hg38 -Ne "select varId,clinSign,scv from clinvarSub" | sort  -S 40g  > clinvarSubSub.txt
+for db in $dbs
+do
+workDir=subLollyBuild$db
+rm -rf $workDir
+mkdir $workDir
+cd $workDir
+bigBedToBed /gbdb/$db/bbi/clinvar/clinvarMain.bb stdout | tawk '{print $40, $1,$2,$2+1,$4}' | sort  -S 40g > sort.main.bed
+hgsql $db -Ne "select varId,clinSign,scv from clinvarSub" | sort  -S 40g  > clinvarSubSub.txt
 
-join -t $'\t' sort.main.bed clinvarSubSub.txt | tawk '{print $2,$3,$4,$5,$6,$1, $7}' | sort -S 40g -k1,1 -k2,2n -k5,5 | tawk -f makeFranklin   | tawk -f assignColors > tmp1
+join -t $'\t' sort.main.bed clinvarSubSub.txt | tawk '{print $2,$3,$4,$5,$6,$1, $7}' | sort -S 40g -k1,1 -k2,2n -k5,5 | tawk -f ../makeFranklin   | tawk -f ../assignColors > tmp1
 # add the line break after v409
 #tawk '{print $1":"$2 + 1"-"$3" <br>Variants (submissions):"$11}' tmp1 > tmp2
 tawk '{print $1":"$2 + 1"-"$3" Variants (submissions):"$11}' tmp1 > tmp2
 paste tmp1 tmp2 > bigBedInput.bed
 
-bedToBigBed -as=$HOME/kent/src/hg/lib/clinvarSubLolly.as -type=bed9+5 -tab bigBedInput.bed /cluster/data/hg38/chrom.sizes clinvarSubLolly.bb
-mkdir -p /gbdb/hg38/clinvarSubLolly
-ln -s `pwd`/clinvarSubLolly.bb /gbdb/hg38/clinvarSubLolly/clinvarSubLolly.bb
+rm -f ../clinvarSubLolly.$db.bb
+bedToBigBed -as=../clinvarSubLolly.as -type=bed9+5 -tab bigBedInput.bed /cluster/data/$db/chrom.sizes ../clinvarSubLolly.$db.bb
 
-bigBedToBed /gbdb/hg38/bbi/clinvar/clinvarMain.bb stdout | tawk '{print $40, $1,$2,$2+1,$4,$13,$15,$18,$19}' | sort  -S 40g > sort.main.bed
-hgsql hg38 -Ne "select * from clinvarSub" | sort  -S 40g  > clinvarSubSub.txt
-join -t $'\t' sort.main.bed clinvarSubSub.txt | tawk '{print $2,$3,$4,$5,0,"+",0,0,"0,0,0",$6,$20,$8, $9,$1,$10,$7,$11,$12,$13,$14,$15,$16,$17,$18,$19,$21}' | sort -S 40g -k1,1 -k2,2n | tawk -f assignScore > bigBedInput.bed
+bigBedToBed /gbdb/$db/bbi/clinvar/clinvarMain.bb stdout | tawk '{print $40, $1,$2,$2+1,$4,$13,$15,$18,$19}' | sort  -S 40g > sort.main.bed
+hgsql $db -Ne "select * from clinvarSub" | sort  -S 40g  > clinvarSubSub.txt
+join -t $'\t' sort.main.bed clinvarSubSub.txt | tawk '{print $2,$3,$4,$5,0,"+",0,0,"0,0,0",$6,$20,$8, $9,$1,$10,$7,$11,$12,$13,$14,$15,$16,$17,$18,$19,$21}' | sort -S 40g -k1,1 -k2,2n | tawk -f ../assignScore > bigBedInput.bed
 
-bedToBigBed -as=clinvarSubBB.as -type=bed9+11 -tab bigBedInput.bed /cluster/data/hg38/chrom.sizes clinvarSub.bb
-ln -s `pwd`/clinvarSub.bb /gbdb/hg38/clinvarSubLolly/clinvarSub.bb
+rm -f ../clinvarSub.$db.bb
+bedToBigBed -as=../clinvarSubBB.as -type=bed9+11 -tab bigBedInput.bed /cluster/data/$db/chrom.sizes ../clinvarSub.$db.bb
+
+cd ..
+
+#validate
+
+mkdir -p /gbdb/$db/clinvarSubLolly
+rm -f /gbdb/$db/clinvarSubLolly/clinvarSubLolly.bb /gbdb/$db/clinvarSubLolly/clinvarSub.bb
+ln -s `pwd`/clinvarSubLolly.$db.bb /gbdb/$db/clinvarSubLolly/clinvarSubLolly.bb
+ln -s `pwd`/clinvarSub.$db.bb /gbdb/$db/clinvarSubLolly/clinvarSub.bb
+
+# archive
+
+rm -rf $workDir
+done