249b307f8e7edcaa916870d673678044c478e953
hiram
  Mon Sep 9 09:59:05 2019 -0700
Adding Ensembl alias with v95 release refs #22425

diff --git src/hg/makeDb/doc/bosTau9/initialBuild.txt src/hg/makeDb/doc/bosTau9/initialBuild.txt
index 4a05a9f..643ccdf 100644
--- src/hg/makeDb/doc/bosTau9/initialBuild.txt
+++ src/hg/makeDb/doc/bosTau9/initialBuild.txt
@@ -460,45 +460,59 @@
     featureBits -countGaps bosTau9 ucscToRefSeq
     # 2715853792 bases of 2715853792 (100.000%) in intersection
 
 #########################################################################
 # add chromAlias table (DONE - 2018-11-08 - Hiram)
     # after ucscToRefSeq and ucscToINSDC tables have been created
 
     mkdir /hive/data/genomes/bosTau9/bed/chromAlias
     cd /hive/data/genomes/bosTau9/bed/chromAlias
 
     hgsql -N -e 'select chrom,name from ucscToRefSeq;' bosTau9 \
         | sort -k1,1 > ucsc.refseq.tab
     hgsql -N -e 'select chrom,name from ucscToINSDC;' bosTau9 \
         | sort -k1,1 > ucsc.genbank.tab
 
+    ### Adding Ensembl alias with v95 release, after idKeys made: 2019-01-16
+    join -t$'\t' ../idKeys/bosTau9.idKeys.txt \
+        ../../ens95/ensBosTau9.idKeys.txt | cut -f2- \
+          | sort -k1,1 | join -t$'\t' <(sort -k1,1 ../../chrom.sizes) - \
+            | awk '{printf "%s\t0\t%d\t%s\n", $1, $2, $3}' \
+               | sort -k1,1 -k2,2n > ucscToEns.bed
+    # Ensembl is missing a chrM sequence:
+    wc -l *.bed
+  2210 ucscToEns.bed
+  2211 ucscToINSDC.bed
+  2211 ucscToRefSeq.bed
+    cut -f1,4 ucscToEns.bed | sort > ucsc.ensembl.tab
+
     ~/kent/src/hg/utils/automation/chromAlias.pl ucsc.*.tab \
 	> bosTau9.chromAlias.tab
 
-for t in refseq genbank
+for t in refseq genbank ensembl
 do
   c0=`cat ucsc.$t.tab | wc -l`
   c1=`grep $t bosTau9.chromAlias.tab | wc -l`
   ok="OK"
   if [ "$c0" -ne "$c1" ]; then
      ok="ERROR"
   fi
   printf "# checking $t: $c0 =? $c1 $ok\n"
 done
 # checking refseq: 2211 =? 2211 OK
 # checking genbank: 2211 =? 2211 OK
+# checking ensembl: 2210 =? 2210 OK
 
     hgLoadSqlTab bosTau9 chromAlias ~/kent/src/hg/lib/chromAlias.sql \
         bosTau9.chromAlias.tab
 
 #########################################################################
 # fixup search rule for assembly track/gold table (DONE - 2018-11-06 - Hiram)
     cd ~/kent/src/hg/makeDb/trackDb/cow/bosTau9
 
     # preview prefixes and suffixes:
     hgsql -N -e "select frag from gold;" bosTau9 \
       | sed -e 's/[0-9][0-9]*//;' | sort | uniq -c | sed -e 's/^/#\t/;'
     #             1 NC_.1
     #          2210 NKLS.1
 
     # implies a rule: 'N[CK][LS0-9_]+(\.[0-9]+)?'