4bd3913b145415c4d24d5c6b2fa9ee5b966257c5
chmalee
  Fri Jul 31 11:44:52 2020 -0700
More clinGen dosage changes after extrernal feedback, refs #24818

diff --git src/hg/utils/otto/clinGen/makeDosage.sh src/hg/utils/otto/clinGen/makeDosage.sh
index 8704a59..2ab4e24 100755
--- src/hg/utils/otto/clinGen/makeDosage.sh
+++ src/hg/utils/otto/clinGen/makeDosage.sh
@@ -1,65 +1,67 @@
 #!/bin/bash
 
 # downloads and builds the curated ClinGen Curated CNVS track
 # assumes running in the build directory:
 # /hive/data/outside/otto/clinGen/
 set -beEu -o pipefail
 
 WORKDIR=$1
 mkdir -p ${WORKDIR}/clinGenDosage
 cd ${WORKDIR}/clinGenDosage
 
 echo "user anonymous
 ls ClinGen*
 bye" > ftp.dosage.cmds
 
 if [ -e release.list ]
 then
     mv release.list prev.release.list
 fi
 touch prev.release.list
 rm -f release.list
 
 # connect and list a directory, result to file: ls.check
 ftp -n -v -i ftp.clinicalgenome.org 2>&1 < ftp.dosage.cmds &> ls.check
 grep "haplo\|triplo\|curation" ls.check | sort > release.list || echo "Error - no bed files found"
 
 # see if anything is changing, if so, notify, download, and build
 diff prev.release.list release.list > release.diff || true
 count=`wc -l release.diff | cut -d' ' -f1`
 if [ "${count}" -gt 1 ]
 then
     echo "New ClinGen Dosage update"
     today=`date +%F`
     mkdir -p ${today}/{download,output}
     cd ${today}/download
     for grc in GRCh37 GRCh38
     do
-        wget -N -q "ftp://ftp.clinicalgenome.org/ClinGen_haploinsufficiency_gene_${grc}.bed"
-        wget -N -q "ftp://ftp.clinicalgenome.org/ClinGen_triplosensitivity_gene_${grc}.bed"
         wget -N -q "ftp://ftp.clinicalgenome.org/ClinGen_region_curation_list_${grc}.tsv"
         wget -N -q "ftp://ftp.clinicalgenome.org/ClinGen_gene_curation_list_${grc}.tsv"
         if [ ${grc} == "GRCh37" ]
         then
             echo $grc
-            ../../../processClinGenDosage.py ClinGen_haploinsufficiency_gene_${grc}.bed ClinGen_gene_curation_list_${grc}.tsv haplo | sort -k1,1 -k2,2n > ../output/hg19.clinGenHaplo.bed
-            ../../../processClinGenDosage.py ClinGen_triplosensitivity_gene_${grc}.bed ClinGen_gene_curation_list_${grc}.tsv triplo | sort -k1,1 -k2,2n > ../output/hg19.clinGenTriplo.bed
-            bedToBigBed -type=bed9+10 -as=../../clinGenDosageHaplo.as -tab ../output/hg19.clinGenHaplo.bed /hive/data/genomes/hg19/chrom.sizes ../output/hg19.clinGenHaplo.bb
-            bedToBigBed -type=bed9+10 -as=../../clinGenDosageTriplo.as -tab ../output/hg19.clinGenTriplo.bed /hive/data/genomes/hg19/chrom.sizes ../output/hg19.clinGenTriplo.bb
+            # the process script creates a haplo.bed and triplo.bed file:
+            ../../../processClinGenDosage.py ClinGen_region_curation_list_${grc}.tsv ClinGen_gene_curation_list_${grc}.tsv ../output/hg19
+            sort -k1,1 -k2,2n ../output/hg19.haplo.bed > ../output/hg19.clinGenHaplo.bed
+            sort -k1,1 -k2,2n ../output/hg19.triplo.bed > ../output/hg19.clinGenTriplo.bed
+            bedToBigBed -type=bed9+13 -as=../../clinGenDosageHaplo.as -tab ../output/hg19.clinGenHaplo.bed /hive/data/genomes/hg19/chrom.sizes ../output/hg19.clinGenHaplo.bb
+            bedToBigBed -type=bed9+13 -as=../../clinGenDosageTriplo.as -tab ../output/hg19.clinGenTriplo.bed /hive/data/genomes/hg19/chrom.sizes ../output/hg19.clinGenTriplo.bb
             cp ../output/hg19.clinGenHaplo.bb ${WORKDIR}/release/hg19/clinGenHaplo.bb
             cp ../output/hg19.clinGenTriplo.bb ${WORKDIR}/release/hg19/clinGenTriplo.bb
         elif [ ${grc} == "GRCh38" ]
         then
             echo $grc
-            ../../../processClinGenDosage.py ClinGen_haploinsufficiency_gene_${grc}.bed ClinGen_gene_curation_list_${grc}.tsv haplo | sort -k1,1 -k2,2n > ../output/hg38.clinGenHaplo.bed
-            ../../../processClinGenDosage.py ClinGen_triplosensitivity_gene_${grc}.bed ClinGen_gene_curation_list_${grc}.tsv triplo | sort -k1,1 -k2,2n > ../output/hg38.clinGenTriplo.bed
-            bedToBigBed -type=bed9+10 -as=../../clinGenDosageHaplo.as -tab ../output/hg38.clinGenHaplo.bed /hive/data/genomes/hg38/chrom.sizes ../output/hg38.clinGenHaplo.bb
-            bedToBigBed -type=bed9+10 -as=../../clinGenDosageTriplo.as -tab ../output/hg38.clinGenTriplo.bed /hive/data/genomes/hg38/chrom.sizes ../output/hg38.clinGenTriplo.bb
+            # the process script creates a haplo.bed and triplo.bed file:
+            ../../../processClinGenDosage.py ClinGen_region_curation_list_${grc}.tsv ClinGen_gene_curation_list_${grc}.tsv ../output/hg38
+            sort -k1,1 -k2,2n ../output/hg38.haplo.bed > ../output/hg38.clinGenHaplo.bed
+            sort -k1,1 -k2,2n ../output/hg38.triplo.bed > ../output/hg38.clinGenTriplo.bed
+            bedToBigBed -type=bed9+13 -as=../../clinGenDosageHaplo.as -tab ../output/hg38.clinGenHaplo.bed /hive/data/genomes/hg38/chrom.sizes ../output/hg38.clinGenHaplo.bb
+            bedToBigBed -type=bed9+13 -as=../../clinGenDosageTriplo.as -tab ../output/hg38.clinGenTriplo.bed /hive/data/genomes/hg38/chrom.sizes ../output/hg38.clinGenTriplo.bb
             cp ../output/hg38.clinGenHaplo.bb ${WORKDIR}/release/hg38/clinGenHaplo.bb
             cp ../output/hg38.clinGenTriplo.bb ${WORKDIR}/release/hg38/clinGenTriplo.bb
         fi
     done
     cd ../..
 else
     echo "No ClinGen CNV update"
 fi