From 8847c5070b5309a066f05b807c2b76f07abbe680 Mon Sep 17 00:00:00 2001
From: Marco van Zwetselaar <zwets@zwets.com>
Date: Tue, 26 Jan 2016 23:33:17 +0300
Subject: [PATCH] Add uf-dress as inverse of uf-bare.

---
 uf-bare  | 30 +++++++++++++++++++---
 uf-dress | 78 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 105 insertions(+), 3 deletions(-)
 create mode 100755 uf-dress

diff --git a/uf-bare b/uf-bare
index 2816c1b..0a9c40b 100755
--- a/uf-bare
+++ b/uf-bare
@@ -29,16 +29,32 @@ usage_exit() {
 	echo
 	echo "Usage: $(basename $0) [OPTIONS] [FILE] ..."
 	echo
-	echo "  Drop the headers and output only the bare sequences from each FILE."
-	echo "  If no FILE is present or FILE is '-', read from standard input."
+	echo "  Output only the bare sequences from each FILE to stanard output, dropping the"
+	echo "  headers.  If no FILE is present or FILE is '-', read from standard input."
+	echo
+	echo "  Options"
+	echo "   -w HDRSFILE   Write the headers to HDRSFILE, which must not already exist."
+	echo "   -f|--force    Overwrite HDRSFILE if it exists."
 	echo 
+	echo "  By default headers go to /dev/null.  Use option -w to store them in a file."
+	echo "  The file can be merged back in with bare sequences using 'uf-dress'."
+	echo
 	exit ${1:-1}
 }
 
 # Parse options
 
+unset HDRSFILE FORCE
+
 while [ $# -ne 0 -a "$(expr "$1" : '\(.\).*')" = "-" ]; do
 	case $1 in
+	-w)	shift
+		[ $# -ge 1 ] || usage_exit
+		HDRSFILE="$1"
+		;;
+	-f|--force)
+		FORCE="yes"
+		;;
 	--help)
 		usage_exit 0
 		;;
@@ -48,5 +64,13 @@ while [ $# -ne 0 -a "$(expr "$1" : '\(.\).*')" = "-" ]; do
 	shift
 done
 
-awk -b -O 'NR%2==0'
+# Check options validity
+
+[ -z "$HDRSFILE" ] || [ -n "$FORCE" ] || [ ! -e "$HDRSFILE" ] || err_exit "file exists (use --force to overwrite): '$HDRSFILE'"
+
+# Do the work
+
+awk -b -O -v F="$HDRSFILE" '
+	NR%2==1 && F { print > "'"$HDRSFILE"'" }
+	NR%2==0' "$@"
 
diff --git a/uf-dress b/uf-dress
new file mode 100755
index 0000000..c737b96
--- /dev/null
+++ b/uf-dress
@@ -0,0 +1,78 @@
+#!/bin/sh
+#
+#  uf-dress - Turn bare sequence data into an unfasta file.
+#  Copyright (C) 2016  Marco van Zwetselaar <io@zwets.it>
+#
+#  This program is free software: you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation, either version 3 of the License, or
+#  (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  You should have received a copy of the GNU General Public License
+#  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+#  Created on 2016-01-25
+
+# Function to exit this script with an error message on stderr
+err_exit() {
+	echo "$(basename "$0"): $*" >&2
+	exit 1
+}
+
+# Function to show usage information and exit
+usage_exit() {
+	echo
+	echo "Usage: $(basename $0) [OPTIONS] [FILE] ..."
+	echo
+	echo "  Insert headers to turn bare sequence FILE(s) into valid unfasta.  If no FILE or"
+	echo "  FILE is '-' read from standard input.  Write unfasta to standard output."
+	echo
+	echo "  Options"
+	echo "   -r HDRSFILE   Optional file to read header lines from.  If not specified then"
+	echo "                 default headers 'lcl|NUM' will be generated."
+	echo
+	echo "  The HDRSFILE could be a file previously written by 'uf-bare', or output from" 
+	echo "  the 'uf-hdrs' filter.  Tip: use bash process substitution to avoid temp files:"
+	echo
+	echo '   $ uf file.fna | uf-bare | ..processing.. | uf-dress -r <(uf file.fna | uf-hdrs)'
+	echo
+	exit ${1:-1}
+}
+
+# Parse options
+
+unset HDRSFILE
+
+while [ $# -ne 0 -a "$(expr "$1" : '\(.\).*')" = "-" ]; do
+	case $1 in
+	-r)	shift
+		[ $# -ge 1 ] || usage_exit
+		HDRSFILE="$1"
+		;;
+	--help)
+		usage_exit 0
+		;;
+	*) usage_exit
+		;;
+	esac
+	shift
+done
+
+# Check options validity
+
+[ -z "$HDRSFILE" ] || [ -r "$HDRSFILE" ] || err_exit "cannot read file: '$HDRSFILE'"
+
+# Do the work
+
+awk -b -O -v F="$HDRSFILE" '{
+	if (F) getline HDR < F; else HDR = ">lcl|" NR
+	print HDR
+	print
+	} 
+	END { if (F) close (F) }' "$@"
+