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Add script to clean up GISAID sequence file for direct use
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Brian Pardy
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Feb 19, 2020
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#!/usr/bin/env bash | ||
set -e | ||
GISAID_SARSCOV2_IN=$1 | ||
GISAID_SARSCOV2_OUT=$2 | ||
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echo "Normalizing GISAID file $GISAID_SARSCOV2_IN to $GISAID_SARSCOV2_OUT" | ||
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# Remove leading 'BetaCoV' and 'BetaCov' from sequence names | ||
# Convert embedded spaces in sequence names to underscore (Hong Kong sequences) | ||
# Remove trailing |EPI_ISL_id|datestamp from sequence names | ||
# Eliminate duplicate sequences (keep only the first seen) | ||
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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"}!x[$1]++{print ">"$0}' | # remove duplicates | ||
grep -v '^>*$' > $GISAID_SARSCOV2_OUT | ||
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