a2c93356f18957d5cea8c5ec44cb005a2ce03d02
hiram
  Fri Jan 15 15:41:54 2021 -0800
LRG track updates refs #24672

diff --git src/hg/makeDb/doc/hg38/hg38.txt src/hg/makeDb/doc/hg38/hg38.txt
index aa41c8b..03a1488 100644
--- src/hg/makeDb/doc/hg38/hg38.txt
+++ src/hg/makeDb/doc/hg38/hg38.txt
@@ -3696,43 +3696,46 @@
     pslCheck lrg.psl
 #checked: 919 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 lrgTranscriptsHg38.psl
     mrnaToGene -genePredExt -cdsFile=lrgTranscripts.cds -keepInvalid \
       lrgTranscriptsHg38.psl lrgTranscriptsHg38NoName2.gp
 #Warning: no CDS for LRG_163t1
 #Warning: no CDS for LRG_347t1
     # It's OK if mrnaToGene complains about "no CDS" for a non-coding tx (RefSeq accession NR_*).
     grep -l NR_ LRG_163.xml LRG_347.xml
 #LRG_163.xml
 #LRG_347.xml
 
+    cat lrgCdna.tab | sed -e 's/^/>/;' | tr '\t' '\n' > lrgCdna.fa
     # construct bigPsl with five extra fields
-    pslToBigPsl lrgTranscriptsHg38.psl bigPsl.txt
+    pslToBigPsl -fa=lrgCdna.fa -cds=lrgTranscripts.cds \
+	lrgTranscriptsHg38.psl bigPsl.txt
 
     # add the five extra identifiers to the bigPsl file:
     join -t$'\t' -1 4 \
        -o 1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8,1.9,1.10,1.11,1.12,1.13,1.14,1.15\
 ,1.16,1.17,1.18,1.19,1.20,1.21,1.22,1.23,1.24,1.25,2.2,2.3,2.4,2.5,2.6,2.7 \
        <(sort -k4 bigPsl.txt) lrgTransExtraFields.tsv \
          | sort -k1,1 -k2,2n > lrgExtraTranscriptsHg38.bigPsl.bed
 
     bedToBigBed -as=bigPsl+6.as -type=bed12+19 -tab \
        lrgExtraTranscriptsHg38.bigPsl.bed ../../../chrom.sizes lrgBigPsl.bb
     bigBedInfo lrgBigPsl.bb
+    rm -f /gbdb/hg38/bbi/lrgBigPsl.bb
     ln -sf `pwd`/lrgBigPsl.bb /gbdb/hg38/bbi
     hgBbiDbLink hg38 lrgBigPsl /gbdb/hg38/bbi/lrgBigPsl.bb
 
 
     # Load PSL, CDS and sequences.
     hgLoadPsl hg38 -table=lrgTranscriptAli lrgTranscriptsHg38.psl
     hgLoadSqlTab hg38 lrgCds ~/kent/src/hg/lib/cdsSpec.sql lrgTranscripts.cds
     hgPepPred hg38 tab lrgCdna lrgCdna.tab
     hgPepPred hg38 tab lrgPep lrgPep.tab
 
 
 #############################################################################
 ## 7-Way Multiz (DONE - 2014-06-02 - Hiram)
     ssh hgwdev
     mkdir /hive/data/genomes/hg38/bed/multiz7way