05e67c59a20a5d00b810a981aef3b00c5bef82e1
max
  Fri Sep 20 06:03:18 2024 -0700
more features to hubtools: search in both parent and subdirs, better docs

diff --git src/hg/makeDb/scripts/prsEmerge/prs2bigBed.sh src/hg/makeDb/scripts/prsEmerge/prs2bigBed.sh
index 7a1420e..409ab13 100644
--- src/hg/makeDb/scripts/prsEmerge/prs2bigBed.sh
+++ src/hg/makeDb/scripts/prsEmerge/prs2bigBed.sh
@@ -1,17 +1,19 @@
 # written by Zia Truong and slightly adapted by Max and committed
 echo "Converting PRS files to BED files..."
 mkdir output
 wait
 
 python3 ~/kent/src/hg/makeDb/scripts/prsEmerge/prs2bed.py # iterates over files in data/, writes to output/
 
 echo "Converting BED files to bigBED files..."
 #looping through files for loop code based on https://stackoverflow.com/a/10523501
 for bed in ./output/*.bed
 do
+  baseName=`basename $bed .bed`
   sort -k1,1 -k2,2n "${bed}" -o "${bed}"
-  bedToBigBed -as=prs.as -type=bed9+2 "${bed}" /hive/data/genomes/hg19/chrom.sizes "${bed}.bb"
+  bedToBigBed -as=prs.as -type=bed9+2 "${bed}" /hive/data/genomes/hg19/chrom.sizes bigBed/${baseName}.bb
   rm ${bed}
 done
 
 echo "Done!"
+echo do not forget symlinks in /gbdb/hg19/prsEmerge/