4d496ac9b43b29987257f6e38b90a03b300922d8
lrnassar
  Thu Dec 16 13:17:07 2021 -0800
Updating name for what files we check on clinGen, refs ChrisL

diff --git src/hg/utils/otto/clinGen/makeDosage.sh src/hg/utils/otto/clinGen/makeDosage.sh
index e7ee818..2cab3ee 100755
--- src/hg/utils/otto/clinGen/makeDosage.sh
+++ src/hg/utils/otto/clinGen/makeDosage.sh
@@ -1,64 +1,64 @@
 #!/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*
+ls ClinGen*curation_list*
 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 db in hg19 hg38
     do
         grc=""
         if [ ${db} == "hg19" ]
         then
             grc="GRCh37"
             wget -N -q "ftp://ftp.clinicalgenome.org/ClinGen_region_curation_list_${grc}.tsv"
             wget -N -q "ftp://ftp.clinicalgenome.org/ClinGen_gene_curation_list_${grc}.tsv"
         elif [ ${db} == "hg38" ]
         then
             grc="GRCh38"
             wget -N -q "ftp://ftp.clinicalgenome.org/ClinGen_region_curation_list_${grc}.tsv"
             wget -N -q "ftp://ftp.clinicalgenome.org/ClinGen_gene_curation_list_${grc}.tsv"
         fi
         echo $grc
         # the process script creates a haplo.bed and triplo.bed file:
         hgsql -Ne "select phenotypeId, description from omimPhenotype" ${db} > ${db}.omimPhenotypes
         ../../../processClinGenDosage.py ClinGen_region_curation_list_${grc}.tsv ClinGen_gene_curation_list_${grc}.tsv ${db}.omimPhenotypes ../output/${db}
         sort -k1,1 -k2,2n ../output/${db}.haplo.bed > ../output/${db}.clinGenHaplo.bed
         sort -k1,1 -k2,2n ../output/${db}.triplo.bed > ../output/${db}.clinGenTriplo.bed
         bedToBigBed -type=bed9+16 -as=../../clinGenDosageHaplo.as -tab ../output/${db}.clinGenHaplo.bed /hive/data/genomes/${db}/chrom.sizes ../output/${db}.clinGenHaplo.bb
         bedToBigBed -type=bed9+16 -as=../../clinGenDosageTriplo.as -tab ../output/${db}.clinGenTriplo.bed /hive/data/genomes/${db}/chrom.sizes ../output/${db}.clinGenTriplo.bb
         cp ../output/${db}.clinGenHaplo.bb ${WORKDIR}/release/${db}/clinGenHaplo.bb
         cp ../output/${db}.clinGenTriplo.bb ${WORKDIR}/release/${db}/clinGenTriplo.bb
     done
     cd ../..
 else
     echo "No ClinGen CNV update"
 fi