7dea7c645f8ce8892d6d4d162a3cf8295309062f
chmalee
  Fri Dec 11 11:22:24 2020 -0800
Bringing repo copies of omim scripts up to date with the working versions, refs #18151

diff --git src/hg/utils/otto/isca/buildISCA.csh src/hg/utils/otto/isca/buildISCA.csh
index 7f0b419..c74781a 100755
--- src/hg/utils/otto/isca/buildISCA.csh
+++ src/hg/utils/otto/isca/buildISCA.csh
@@ -1,91 +1,99 @@
 #!/bin/tcsh -e
 # assumes running in build directory
 set db=$1
 
 if "$db" == "hg19" then
     set grc=GRCh37
-    set liftUp=cat
+    set liftUp="liftUp -type=.bed stdout ../../hg19.lift warn stdin"
 else if "$db" == "hg38" then
     set grc=GRCh38
-    set liftUp="liftUp -type=.bed stdout /cluster/data/hg38/jkStuff/dbVar.lift warn stdin"
+    set liftUp="liftUp -type=.bed stdout ../../hg38.lift warn stdin"
 else if "$db" == "hg18" then
+    # left unchanged, as we no longer build this for hg18.  If that changes, we'd need to build a liftUp file
+    # to translate the chromosome names.
     set grc=NCBI36
     set liftUp=cat
+else
+    echo "Unfamiliar assembly: $db - please edit the script to provide the correct GRC name and liftUp command"
+    exit 1;
 endif
 
 cd $1
 
 # set today = `date +%Y_%m_%d`
 # mkdir /hive/data/genomes/hg19/bed/isca/$today
 # cd /hive/data/genomes/hg19/bed/isca/$today
 
 # Get variants submitted on this assembly, and variants remapped from other assemblies.
 setenv LANG C
 
-# ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/by_study/nstd37_ClinGen_Laboratory-Submitted/gvf/
-# ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/by_study/nstd101_ClinGen_Kaminsky_et_al_2011/gvf/
-# ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/by_study/nstd45_ClinGen_Curated_Dosage_Sensitivity_Map/gvf/
-
-wget -N -q "ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/by_study/nstd37_ClinGen_Laboratory-Submitted/gvf/nstd37_ClinGen_Laboratory-Submitted.${grc}.*.all.germline.ucsc.gvf.gz"
-wget -N -q "ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/by_study/nstd45_ClinGen_Curated_Dosage_Sensitivity_Map/gvf/nstd45_ClinGen_Curated_Dosage_Sensitivity_Map.${grc}.*.all.germline.ucsc.gvf.gz"
-wget -N -q "ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/by_study/nstd101_ClinGen_Kaminsky_et_al_2011/gvf/nstd101_ClinGen_Kaminsky_et_al_2011.${grc}.*.all.germline.ucsc.gvf.gz"
-
-# Remove patch contig mappings; we don't display them anyway.
-rm -f *.p*.gvf.gz
-
+wget -N -q "ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/by_study/gvf/nstd37.${grc}.variant*.gvf.gz"
+wget -N -q "ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/by_study/gvf/nstd101.${grc}.variant*.gvf.gz"
+wget -N -q "ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/by_study/gvf/nstd45.${grc}.variant*.gvf.gz"
 
-zcat nstd101*.gvf.gz nstd37_ClinGen_Laboratory-Submitted*.gvf.gz | ../../gvfToBed8Attrs.pl | $liftUp | sort > foo
+zcat nstd101*.gvf.gz nstd37*.gvf.gz | ../../gvfToBed8Attrs.pl | $liftUp | sort > foo
 
+# Not sure why this step exists.  It appears to just be a chromosome filter, but that's effectively already done ...
 join ../../chromInfo.$db foo -t '	' > isca.bed
 
-zcat nstd45_*.gvf.gz | ../../gvfToBed8Attrs.pl | $liftUp | sort > foo
+zcat nstd45*.gvf.gz | ../../gvfToBed8Attrs.pl | $liftUp | sort > foo
 
+# Not sure why this step exists (as above).  It appears to just be a chromosome filter, but that's effectively already done ...
 join ../../chromInfo.$db foo -t '	' > iscaCurated.bed
+rm -f foo
 
 foreach subtrack (Benign Pathogenic)
   grep -w  $subtrack isca.bed > isca$subtrack.bed
+  echo -n "Loading isca${subtrack}New and iscaCurated${subtrack}New ... "
   hgLoadBed -tab -renameSqlTable -sqlTable=$HOME/kent/src/hg/lib/bed8Attrs.sql \
-    -allowStartEqualEnd $db isca"$subtrack"New isca$subtrack.bed
+    -allowStartEqualEnd $db isca"$subtrack"New isca$subtrack.bed >&/dev/null
   grep -w  $subtrack iscaCurated.bed > iscaCurated$subtrack.bed
   hgLoadBed -tab -renameSqlTable -sqlTable=$HOME/kent/src/hg/lib/bed8Attrs.sql \
-    -allowStartEqualEnd $db iscaCurated"$subtrack"New iscaCurated$subtrack.bed
+    -allowStartEqualEnd $db iscaCurated"$subtrack"New iscaCurated$subtrack.bed >&/dev/null
+  echo "Success"
 end
 
 # The subcategories of Uncertain need a bit more sophisticated treatment:
 set subtrack = Uncertain
 grep -w $subtrack isca.bed \
 | grep -vi 'Uncertain Significance: likely' \
   > isca$subtrack.bed
+echo -n "Loading isca${subtrack}New ... "
 hgLoadBed -tab -renameSqlTable -sqlTable=$HOME/kent/src/hg/lib/bed8Attrs.sql \
-  -allowStartEqualEnd $db isca"$subtrack"New isca$subtrack.bed
+  -allowStartEqualEnd $db isca"$subtrack"New isca$subtrack.bed >&/dev/null
+echo "Success"
 
 foreach unc (benign pathogenic)
   set subtrack = Likely`perl -we 'print ucfirst("'$unc'");'`
   grep -wi "Likely $unc" isca.bed \
     > isca$subtrack.bed
+  echo -n "Loading isca${subtrack}New ... "
   hgLoadBed -tab -renameSqlTable -sqlTable=$HOME/kent/src/hg/lib/bed8Attrs.sql \
-    -allowStartEqualEnd $db isca"$subtrack"New isca$subtrack.bed
+    -allowStartEqualEnd $db isca"$subtrack"New isca$subtrack.bed >&/dev/null
+  echo "Success"
 end
 
 # make bedGraphs
 hgsql -N -e "SELECT chrom, chromStart, chromEnd FROM iscaPathogenicNew \
     WHERE attrVals LIKE '%number_gain%'" $db | sort \
 | bedItemOverlapCount $db stdin > iscaPathGain.bedGraph
 
 hgsql -N -e "SELECT chrom, chromStart, chromEnd FROM iscaPathogenicNew \
     WHERE attrVals LIKE '%number_loss%'" $db | sort \
 | bedItemOverlapCount $db stdin > iscaPathLoss.bedGraph
 
 hgsql -N -e "SELECT chrom, chromStart, chromEnd FROM iscaBenignNew \
     WHERE attrVals LIKE '%number_gain%'" $db | sort \
 | bedItemOverlapCount $db stdin > iscaBenignGain.bedGraph
 
 hgsql -N -e "SELECT chrom, chromStart, chromEnd FROM iscaBenignNew \
     WHERE attrVals LIKE '%number_loss%'" $db | sort \
 | bedItemOverlapCount $db stdin > iscaBenignLoss.bedGraph
 
 # load tables
-hgLoadBed -bedGraph=4 $db iscaPathGainCumNew iscaPathGain.bedGraph
-hgLoadBed -bedGraph=4 $db iscaPathLossCumNew iscaPathLoss.bedGraph
-hgLoadBed -bedGraph=4 $db iscaBenignGainCumNew iscaBenignGain.bedGraph
-hgLoadBed -bedGraph=4 $db iscaBenignLossCumNew iscaBenignLoss.bedGraph
+echo -n "Loading bedGraphs ... "
+hgLoadBed -bedGraph=4 $db iscaPathGainCumNew iscaPathGain.bedGraph >&/dev/null
+hgLoadBed -bedGraph=4 $db iscaPathLossCumNew iscaPathLoss.bedGraph >&/dev/null
+hgLoadBed -bedGraph=4 $db iscaBenignGainCumNew iscaBenignGain.bedGraph >&/dev/null
+hgLoadBed -bedGraph=4 $db iscaBenignLossCumNew iscaBenignLoss.bedGraph >&/dev/null
+echo "Success"