Add normalize_gisaid_fasta.sh for issue nextstrain#53

scripts/normalize_gisaid_fasta.sh

@@ -0,0 +1,35 @@
+#!/usr/bin/env bash
+set -e 
+GISAID_SARSCOV2_IN=$1
+GISAID_SARSCOV2_OUT=$2
+MIN_LENGTH=$3
+
+if [[ ! -r "$GISAID_SARSCOV2_IN" ]]
+then
+	echo "$0: input $GISAID_SARSCOV2_IN not found"
+	exit 1
+fi
+
+if [[ -z "$MIN_LENGTH" ]]
+then
+	echo "Using default minimum length of 15000"
+	MIN_LENGTH=15000
+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 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 $GISAID_SARSCOV2_IN | 
+	sed 's/^>BetaCoV\//>/gi' |	# remove leading BetaCo[vV]
+	sed 's/ //g' |			# remove embedded spaces
+	sed 's/|.*$//' | 		# remove trailing metadata
+	awk "BEGIN{RS=\">\";FS=\"\n\"}length>$MIN_LENGTH{print \">\"\$0}" |	# remove short seqs
+	awk 'BEGIN{RS=">";FS="\n"}!x[$1]++{print ">"$0}' | 	# remove duplicates
+	grep -v '^>*$' > $GISAID_SARSCOV2_OUT
+
+exit 0