48578d7724625cda2499bd11f8b6ce19463a1279
braney
  Fri Sep 2 15:24:25 2022 -0700
HGNC track is ready for QA.

diff --git src/hg/makeDb/doc/hg38/hgnc.txt src/hg/makeDb/doc/hg38/hgnc.txt
index 1c8f4aa..6606642 100644
--- src/hg/makeDb/doc/hg38/hgnc.txt
+++ src/hg/makeDb/doc/hg38/hgnc.txt
@@ -1,51 +1,60 @@
 mkdir -p /cluster/data/hg38/bed/hgnc
 cd /cluster/data/hg38/bed/hgnc
 
-# get the data
+# get the HGNC data
 wget "http://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/tsv/hgnc_complete_set.txt"
 
-# generate trix file with symbol, alias, and previos values
+# get the Entrez data
+wget "https://ftp.ncbi.nih.gov/gene/DATA/gene2accession.gz"
+gunzip gene2accession.gz
+
+# separate human accessions in the Entrez data
+grep "^9606" gene2accession >  human.gene2accession
+
+# collect all the mappings to hg38 (these have NCBI chromosome names)
+grep GRCh38 human.gene2accession  | tawk '{print $2, $8,$10,$11}' | sort | uniq > entrezToLocNcbi.txt
+
+# substitute UCSC names
+tawk '{print $1,$2}' /cluster/data/hg38/hg38.chromAlias.tsv > ncbiToUcsc.map
+subColumn -skipMiss -miss=idMiss.txt 2 entrezToLocNcbi.txt ncbiToUcsc.map entrezToLoc.txt
+
+# generate trix file with symbol, alias, and previous values
 tail -n +2 hgnc_complete_set.txt | tawk '{print $1, $2 " " $9 " " $11;}' | tr -d '"' | tr '|' ' ' > trixInput.txt
 ixIxx trixInput.txt search.hg38.ix search.hg38.ixx
 
-# look at field names and create proto AS file
+# look at field names and create proto AS file (just done the first time)
 #tawk '{for(ii=1;  ii <= NF; ii++) print ii, $ii; exit}' hgnc_complete_set.txt
 #tawk '{for(ii=1;  ii <= NF; ii++) printf "\tstring %s; \"%s\"\n", $ii,$ii; exit}' *comple* > asSkeleton.as
 
 # create input file without header and sorted by first field ( HGNC:### )
 tail -n +2 hgnc_complete_set.txt | sort -k 1b,1 > input.txt
 
 # put black for every type for the moment.  This should be based on GENCODE colors
 tawk '{print $5}' input.txt | sort -u | awk '{printf "s/%s/0,0,0/\n", $0}' > color.sed.txt
-tawk '{print $1,$5}' input.txt | sed -f color.sed.txt | sort -k 1b,1 > id.color.txt
-join -j 1 -t $'\t' input.txt id.color.txt > inputColor.txt
-
-# put refseq ID as first field for joins
-tawk '{if ($24 != "")  print $24,$0}' inputColor.txt | sort -k 1b,1 > refSeq.hgnc.txt
 
-# get NG_* positions from LRG track
-bigBedToBed /gbdb/hg38/bbi/lrg.bb stdout | tawk '{split($18,a,"."); print a[1],$1,$2,$3}' | sort -k 1b,1 > refSeqGene.hg38.txt
+#manually fixed colors for coding, pseudogene, and non-coding
+tawk '{print $1,$5}' input.txt | sed -f color.sed.txt | sort -k 1b,1 > id.color.txt
 
-# get NM, NR, XR, XM, YP, etc from ncbiRefSeq track
-hgsql hg38 -Ne "select * from ncbiRefSeq" | tawk '{split($2,a,"."); print a[1],$3,$5,$6}' | sort -k 1b,1 > refSeq.hg38.txt
+# build hgnc file with assigned colors as the 58th field
+join -j 1 -t $'\t' input.txt id.color.txt > inputColor.txt
 
-# merge positions
-sort -k 1b,1 refSeqGene.hg38.txt refSeq.hg38.txt > refSeq.all.hg38.txt
+# put entrez ID as first field for joins
+tawk '{if ($19 != "")  print $19,$0}' inputColor.txt | sort -k 1b,1 > entrez.hgnc.txt
 
 # add position information to HGNC information
-join -j 1 -t $'\t' refSeq.all.hg38.txt refSeq.hgnc.txt | cut -f 2- > positioned.hg38.txt
+join -j 1 -t $'\t' entrezToLoc.txt  entrez.hgnc.txt | cut -f 2- > positioned.hg38.txt
 
 # build first nine fields of bigbed
 tawk '{print $1, $2, $3, $4, 0, "+", 0,0, $58}' positioned.hg38.txt > tmp1
 
 # add the rest of the HGNC fields as extra fields except the id and color which are in the first nine
 tawk '{for(ii=5; ii <= 56; ii++) printf("%s\t", $ii); print $ii}' positioned.hg38.txt > tmp2
 paste tmp1 tmp2 | sort -k1,1 -k2,2n > input.bed
 
 # let's do this thing!
 bedToBigBed -extraIndex=name -tab -type=bed9+53 input.bed /cluster/data/hg38/chrom.sizes hgnc.hg38.bb -as=$HOME/kent/src/hg/lib/hgncBig62.as
 
 # put the files into /gbdb
 mkdir -p /gbdb/hg38/hgnc
 rm -rf /gbdb/hg38/hgnc/hgnc.bb
 ln -s `pwd`/hgnc.hg38.bb /gbdb/hg38/hgnc/hgnc.bb