27d9d88ca49e60586c2d0b211971c8a360d862ac
hiram
  Thu Sep 8 23:00:48 2022 -0700
sequenceName alias should properly be called assembly no redmine

diff --git src/hg/makeDb/doc/panPan3/initialBuild.txt src/hg/makeDb/doc/panPan3/initialBuild.txt
index 52840d4..70f90bd 100644
--- src/hg/makeDb/doc/panPan3/initialBuild.txt
+++ src/hg/makeDb/doc/panPan3/initialBuild.txt
@@ -439,63 +439,63 @@
 
 #########################################################################
 # add chromAlias table (DONE - 2020-06-12 - Hiram)
 
     mkdir /hive/data/genomes/panPan3/bed/chromAlias
     cd /hive/data/genomes/panPan3/bed/chromAlias
 
     hgsql -N -e 'select chrom,name from ucscToRefSeq;' panPan3 \
         | sort -k1,1 > ucsc.refseq.tab
     hgsql -N -e 'select chrom,name from ucscToINSDC;' panPan3 \
         | sort -k1,1 > ucsc.genbank.tab
 
     grep -v "^#" \
       ../../refseq/G*0_assembly_report.txt \
        | awk -F$'\t' '{printf "%s\t%s\n", $7,$1}' \
-         | sort > refseq.sequenceName.txt
+         | sort > refseq.assembly.txt
 
     # do *not* need the ones that have identical names to UCSC names
-    join -2 2 -t$'\t' refseq.sequenceName.txt <(sort -k2,2 ucsc.refseq.tab) \
+    join -2 2 -t$'\t' refseq.assembly.txt <(sort -k2,2 ucsc.refseq.tab) \
       | awk -F$'\t' '{printf "%s\t%s\n", $3, $2}' \
-        | awk -F$'\t' '$1 != $2' | sort > ucsc.sequenceName.tab
+        | awk -F$'\t' '$1 != $2' | sort > ucsc.assembly.tab
 
     wc -l *.tab | sed -e 's/^/#   /;'
 #     4293 ucsc.genbank.tab
 #     4293 ucsc.refseq.tab
-#     4271 ucsc.sequenceName.tab
+#     4271 ucsc.assembly.tab
 
     ~/kent/src/hg/utils/automation/chromAlias.pl ucsc.*.tab \
         > panPan3.chromAlias.tab
 
-for t in refseq genbank sequenceName
+for t in refseq genbank assembly
 do
   c0=`cat ucsc.$t.tab | wc -l`
   c1=`grep $t panPan3.chromAlias.tab | wc -l`
   ok="OK"
   if [ "$c0" -ne "$c1" ]; then
      ok="ERROR"
   fi
   printf "# checking $t: $c0 =? $c1 $ok\n"
 done
 # checking refseq: 4293 =? 4293 OK
 # checking genbank: 4293 =? 4293 OK
-# # checking sequenceName: 4271 =? 4271 OK
+# # checking assembly: 4271 =? 4271 OK
 
     # verify chrM is here properly:
     grep chrM panPan3.chromAlias.tab  | sed -e 's/^/# /;'
 # D38116.1        chrM    genbank
-# MT      chrM    sequenceName
+# MT      chrM    assembly
 # NC_001644.1     chrM    refseq
 
     hgLoadSqlTab panPan3 chromAlias ~/kent/src/hg/lib/chromAlias.sql \
         panPan3.chromAlias.tab
 
 #########################################################################
 # fixup search rule for assembly track/gold table (DONE - 2020-06-12 - Hiram)
     cd ~/kent/src/hg/makeDb/trackDb/bonobo/panPan3
     # preview prefixes and suffixes:
     hgsql -N -e "select frag from gold;" panPan3 \
       | sed -e 's/[0-9][0-9]*//;' | sort | uniq -c | sed -e 's/^/#  /;'
 #        1 NC_.1
 #     4975 SSBP.1
 
     # implies a rule: '[NS][CS][B0-9_][P0-9][0-9]+(\.[0-9]+)?'