normalize_gisaid_fasta.sh

#!/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 25000"
 MIN_LENGTH=25000
fi

echo"Normalizing GISAID file $GISAID_SARSCOV2_IN to $GISAID_SARSCOV2_OUT (min length $MIN_LENGTH)"

# 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 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
 awk 'BEGIN{RS=">";FS="\n"}!x[$1]++{print ">"$0}'|# remove duplicates
 grep -v '^>*$'>$GISAID_SARSCOV2_OUT

exit 0