c67f70fced286da481cf4a3c73013d1d2fca909b
max
  Fri Jul 1 07:07:13 2022 -0700
adding lrg ncbi accession to search specs, refs #29689

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index 43e2b7e..208ba0f 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -28474,30 +28474,31 @@
     string hgvsProt;         "protein HGVS"
     string lastEval;         "last evaluation"
     string guidelines;         "guidelines"
     lstring otherIds;         "other identifiers (OMIM)"
     )
 '_EOF_'
 
 bedToBigBed clinvarMain.bed /scratch/data/hg19/chrom.sizes clinvarMain.bb -type=bed4+18 -tab -as=clinvar.as
 bedToBigBed clinvarCnv.bed /scratch/data/hg19/chrom.sizes clinvarCnv.bb -type=bed4+18 -tab -as=clinvar.as
 cp clinvarMain.bb /hive/data/genomes/hg19/bed/clinvar/
 cp clinvarCnv.bb /hive/data/genomes/hg19/bed/clinvar/
 
 _EOF_
 #########################################################################
 # LOCUS REFERENCE GENOMIC (LRG) REGIONS AND TRANSCRIPTS (DONE 10/25/19 angie)
+# THIS IS NOW AN OTTO JOB !
 # Redmine #13359, #24285 -- otto-mate To Do #17877
 # previously done 7/7/14, 9/9/16, 5/30/18
     screen -S lrg -t lrg
     set today = `date +%Y_%m_%d`
     mkdir -p /hive/data/genomes/hg19/bed/lrg/$today
     cd /hive/data/genomes/hg19/bed/lrg/$today
     wget ftp://ftp.ebi.ac.uk/pub/databases/lrgex/LRG_public_xml_files.zip
     unzip LRG_public_xml_files.zip
     # The .atree file was useful for getting a handle on the hierarchy and types of nodes:
     # autoDtd LRG_1.xml lrg.dtd lrg.stats -atree=lrg.atree
 
     # Run script to convert LRG*.xml files to BED+ for regions and genePredExt+fa for transcripts:
     ~/kent/src/hg/utils/automation/parseLrgXml.pl GRCh37
     genePredCheck lrgTranscriptsUnmapped.gp
 #Error: lrgTranscriptsUnmapped.gp:765: LRG_7t1 no exonFrame on CDS exon 46
@@ -28507,32 +28508,35 @@
     # Contact Variation team leader Fiona Cunningham @EBI to resolve in the background
     # (missing exonFrame info doesn't affect our track representation because we end up using
     # psl).  We agreed to disagree about exon 46 of LRG_7t1 because that last coding exon
     # portion is only the stop codon.
 
     # hg19 has patches on hgwdev but not on the RR, and the patches may remain on hgwdev.
     # To avoid confusion, exclude patch sequences for now; if we release patches, rebuild
     # LRG tracks without this part.
     mv lrg.bed lrg.allSeqs.bed
     cut -f 1 ../../../chrom.sizes.initial | grep -Fwf - lrg.allSeqs.bed > lrg.bed
     wc -l lrg*bed
 #   930 lrg.allSeqs.bed
 #   888 lrg.bed
 
     # Load LRG regions:
+    #bedToBigBed lrg.bed /hive/data/genomes/hg19/chrom.sizes lrg.bb \
+    #-tab -type=bed12+ -as=$HOME/kent/src/hg/lib/lrg.as -extraIndex=name
+    # adding ncbi acc field to search, ML #29689, Max July 1st 2022
     bedToBigBed lrg.bed /hive/data/genomes/hg19/chrom.sizes lrg.bb \
-      -tab -type=bed12+ -as=$HOME/kent/src/hg/lib/lrg.as -extraIndex=name
+         -tab -type=bed12+ -as=$HOME/kent/src/hg/lib/lrg.as -extraIndex=name,ncbiAcc
     ln -sf `pwd`/lrg.bb /gbdb/hg19/bbi/lrg.bb
     hgBbiDbLink hg19 lrg /gbdb/hg19/bbi/lrg.bb
 
     # Map LRG fixed_annotation transcripts from LRG coords to hg19 coords (HT MarkD):
     lrgToPsl lrg.bed /hive/data/genomes/hg19/chrom.sizes lrg.psl
     pslCheck lrg.psl
 #checked: 888 failed: 0 errors: 0
     awk '{print $10 "\t" $11;}' lrg.psl > lrg.sizes
     genePredToFakePsl -chromSize=lrg.sizes placeholder \
       lrgTranscriptsUnmapped.gp lrgTranscriptsFakePsl.psl lrgTranscripts.cds
     pslMap lrgTranscriptsFakePsl.psl lrg.psl lrgTranscriptsHg19.psl
     mrnaToGene -genePredExt -cdsFile=lrgTranscripts.cds -keepInvalid \
       lrgTranscriptsHg19.psl lrgTranscriptsHg19NoName2.gp
 #Warning: no CDS for LRG_163t1
 #Warning: no CDS for LRG_347t1