ad6e3b51842fe726bb9b14e3b0025e59ef9fda17
angie
  Fri Oct 15 09:48:41 2021 -0700
More items for cleanGenBank to detect & substitute.

diff --git src/hg/utils/otto/sarscov2phylo/util.sh src/hg/utils/otto/sarscov2phylo/util.sh
index 8d5182c..1b8e260 100755
--- src/hg/utils/otto/sarscov2phylo/util.sh
+++ src/hg/utils/otto/sarscov2phylo/util.sh
@@ -27,32 +27,34 @@
 export -f fastaSeqCount
 
 cleanGenbank () {
     sed -re 's@Severe acute respiratory syndrome coronavirus 2 SARS-CoV-2/@@;' $* \
     | sed -re 's@Severe acute respiratory syndrome coronavirus 2 isolate SARS[ -]Co[Vv]-2/(human|homo ?sapiens)/@@;' \
     | sed -re 's@Mutant Severe acute respiratory syndrome coronavirus 2 clone SARS-CoV-2[_-]@@;' \
     | sed -re 's@Severe acute respiratory syndrome coronavirus 2( isolate)?( 2019_nCoV)?@@;' \
     | sed -re '/^[A-Z]+$/bx; s@[A-Za-z0-9]+ [a-z]*protein.*@@; :x;' \
     | sed -re 's@(( genomic)? RNA)?, ((nearly )?complete|partial) genome$@@;' \
     | sed -re 's@genome assembly(, complete genome)?: monopartite$@@;' \
     | sed -re 's@ (1 |nasopharyngeal )?genome assembly, chromosome: .*$@@;' \
     | sed -re 's@, complete sequence@@;' \
     | sed -re 's@humans, [A-Za-z]+,( [0-9]+ Years old)?( Adult)?/@@' \
     | sed -re 's@hCo[vV]-19/@@;' \
     | sed -re 's@SARS?-CoV-?2/([Hh]umai?ns?|[Hh]o[mw]o ?sapiens?)/@@;' \
-    | sed -re 's@SARS-CoV-2/(environment|ENV)/@env/@;' \
-    | sed -re 's@SARS-CoV-2/Felis catus/@cat/@;' \
+    | sed -re 's@SARS-CoV-2/HUMAN/@@;' \
+    | sed -re 's@SARS-CoV-2/([Ee]nvironment|ENV)/@env/@;' \
+    | sed -re 's@SARS-CoV-2/Canis lupus familiaris/@dog/@;' \
+    | sed -re 's@SARS-CoV-2/Felis [Cc]atus/@cat/@;' \
     | sed -re 's@SARS-CoV-2/Panthera leo/@lion/@;' \
     | sed -re 's@SARS-CoV-2/Panthera tigris/@tiger/@;' \
     | sed -re 's@SARS-CoV-2/@@;' \
     | sed -re 's@BetaCoV/@@;' \
     | sed -re 's@Homo sapines/@@;' \
     | sed -re 's@ \| @ \|@; s@ $@@; s@[:,]@ @g; s@  @ @g; s@[()]@@g;' \
     | sed -re 's@ \|@\t@;'
 # Got rid of this:   s/ ([^|])/_\1/g;
 }
 export -f cleanGenbank
 
 cleanCncb () {
     sed -re "s@^BetaCoV/@@;
              s@^hCoV-19/@@;
              s@^SARS-CoV-2/@@;