Fix obsolete BetaCoV strings in comments
@@ -18,14 +18,14 @@ fi
echo "Normalizing GISAID file $GISAID_SARSCOV2_IN to $GISAID_SARSCOV2_OUT (min length $MIN_LENGTH)"
-# Remove leading 'BetaCoV' and 'BetaCov' from sequence names
+# Remove leading virus name prefix from sequence names
# Remove embedded spaces in sequence names (Hong Kong sequences)
# Remove trailing |EPI_ISL_id|datestamp from sequence names
# Remove sequences shorter than minimum length
# Eliminate duplicate sequences (keep only the first seen)
#cat $GISAID_SARSCOV2_IN |
- sed 's/^>[hn]Co[Vv]-19\//>/g' $GISAID_SARSCOV2_IN | # remove leading BetaCo[vV]
+ sed 's/^>[hn]Co[Vv]-19\//>/g' $GISAID_SARSCOV2_IN | # remove leading prefix
sed 's/ //g' | # remove embedded spaces
sed 's/|.*$//' | # remove trailing metadata
awk "BEGIN{RS=\">\";FS=\"\n\"}length>$MIN_LENGTH{print \">\"\$0}" | # remove short seqs
