6684918996cf61c1d1a7fb5ee3e6cb3a8a23f083
hiram
  Fri Feb 18 09:27:46 2022 -0800
version 0 before beginning modifications refs #28930

diff --git src/hg/gar/ucscEquiv.sh src/hg/gar/ucscEquiv.sh
new file mode 100755
index 0000000..63dbab2
--- /dev/null
+++ src/hg/gar/ucscEquiv.sh
@@ -0,0 +1,45 @@
+#!/bin/bash
+
+set -beEu -o pipefail
+
+hgsql -N -hgenome-centdb -e 'select name from dbDb where active=1;' hgcentral \
+   | sort > rr.active.list
+
+hgsql -N -e 'SELECT source,destination FROM asmEquivalent WHERE
+  sourceAuthority="ucsc" AND destinationAuthority="refseq" AND
+ matchCount=sourceCount;' hgFixed | sort -u > ucsc.refseq.list
+
+join -t$'\t' rr.active.list ucsc.refseq.list > rr.refseq.equiv.list
+join -v1 -t$'\t' rr.active.list ucsc.refseq.list > rr.not.refseq.list
+
+hgsql -N -e 'SELECT source,destination FROM asmEquivalent WHERE
+  sourceAuthority="ucsc" AND destinationAuthority="genbank" AND
+ matchCount=sourceCount;' hgFixed | sort -u > ucsc.check.genbank.list
+
+join -t$'\t' rr.not.refseq.list ucsc.check.genbank.list > ucsc.genbank.list
+join -t$'\t' rr.active.list ucsc.genbank.list > rr.genbank.equiv.list
+
+cut -f1 ucsc.refseq.list ucsc.genbank.list | sort -u \
+   | join -v1 rr.active.list - > ucsc.rr.not.perfect
+
+hgsql -N -e 'SELECT source,destination FROM asmEquivalent WHERE
+  sourceAuthority="ucsc" AND destinationAuthority="refseq" AND
+ 1=ABS(matchCount-sourceCount);' hgFixed | sort -u \
+   | join -t$'\t' ucsc.rr.not.perfect - > ucsc.rr.refseq.oneMismatch.list
+
+hgsql -N -e 'SELECT source,destination FROM asmEquivalent WHERE
+  sourceAuthority="ucsc" AND destinationAuthority="genbank" AND
+ 1=ABS(matchCount-sourceCount);' hgFixed | sort -u \
+   | join -t$'\t' ucsc.rr.not.perfect - > ucsc.check.genbank.oneMismatch.list
+
+cut -f1 ucsc.rr.refseq.oneMismatch.list \
+   | join -t$'\t' -v2 - ucsc.check.genbank.oneMismatch.list \
+      > ucsc.rr.genbank.oneMismatch.list
+
+sort rr.refseq.equiv.list rr.genbank.equiv.list \
+  ucsc.rr.refseq.oneMismatch.list ucsc.rr.genbank.oneMismatch.list \
+     > rr.GCF.GCA.list
+
+cut -f1 rr.refseq.equiv.list rr.genbank.equiv.list \
+  ucsc.rr.refseq.oneMismatch.list ucsc.rr.genbank.oneMismatch.list \
+    | sort > rr.matched