--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastx_toolkit-0.0.6/scripts/fastq_quality_boxplot_graph.sh	Thu Aug 14 04:52:17 2014 -0400
@@ -0,0 +1,94 @@
+#!/bin/sh
+
+#    FASTX-toolkit - FASTA/FASTQ preprocessing tools.
+#    Copyright (C) 2009  A. Gordon (gordon@cshl.edu)
+#
+#   This program is free software: you can redistribute it and/or modify
+#   it under the terms of the GNU Affero 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 Affero General Public License for more details.
+#
+#    You should have received a copy of the GNU Affero General Public License
+#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+function usage()
+{
+	echo "Solexa-Quality BoxPlot plotter"
+	echo "Generates a solexa quality score box-plot graph "
+	echo
+	echo "Usage: $0 [-i INPUT.TXT] [-t TITLE] [-p] [-o OUTPUT]"
+	echo
+	echo "  [-p]           - Generate PostScript (.PS) file. Default is PNG image."
+	echo "  [-i INPUT.TXT] - Input file. Should be the output of \"solexa_quality_statistics\" program."
+	echo "  [-o OUTPUT]    - Output file name. default is STDOUT."
+	echo "  [-t TITLE]     - Title (usually the solexa file name) - will be plotted on the graph."
+	echo
+	exit 
+}
+
+#
+# Input Data columns: #pos	cnt	min	max	sum       	mean	Q1	med	Q3	IQR	lW	rW A_Count	C_Count	G_Count	T_Count	N_Count
+#  As produced by "solexa_quality_statistics" program
+
+TITLE=""					# default title is empty
+FILENAME=""
+OUTPUTTERM="set term png size 2048,768"		# default output terminal is "PNG"
+OUTPUTFILE="/dev/stdout"   			# Default output file is simply "stdout"
+while getopts ":t:i:o:ph" Option
+	do
+	case $Option in
+		# w ) CMD=$OPTARG; FILENAME="PIMSLogList.txt"; TARGET="logfiles"; ;;
+		t ) TITLE="for $OPTARG" ;;
+		i ) FILENAME=$OPTARG ;;
+		o ) OUTPUTFILE="$OPTARG" ;;
+		p ) OUTPUTTERM="set term postscript enhanced color \"Helvetica\" 8" ;;
+		h ) usage ;;
+		* ) echo "unrecognized argument. use '-h' for usage information."; exit -1 ;;
+	esac
+done
+shift $(($OPTIND - 1)) 
+
+
+if [ "$FILENAME" == "" ]; then
+	usage
+fi
+
+if [ ! -r "$FILENAME" ]; then
+	echo "Error: can't open input file ($1)." >&2
+	exit 1
+fi
+
+#Read number of cycles from the stats file (each line is a cycle, minus the header line)
+#But for the graph, I want xrange to reach (num_cycles+1), so I don't subtract 1 now.
+NUM_CYCLES=$(cat "$FILENAME" | wc -l) 
+
+GNUPLOTCMD="
+$OUTPUTTERM
+set boxwidth 0.8 
+set size 1,1
+set key Left inside
+set xlabel \"read position\"
+set ylabel \"Quality Score (Solexa Scale: 40=Highest, -15=Lowest)\"
+set title  \"Quality Scores $TITLE\"
+#set auto x
+set bars 4.0
+set xrange [ 0: $NUM_CYCLES ]
+set yrange [-15:45]
+set y2range [-15:45]
+set xtics 1 
+set x2tics 1
+set ytics 2
+set y2tics 2
+set tics out
+set grid ytics
+set style fill empty
+plot '$FILENAME' using 1:7:11:12:9 with candlesticks lt 1  lw 1 title 'Quartiles' whiskerbars, \
+      ''         using 1:8:8:8:8 with candlesticks lt -1 lw 2 title 'Medians'
+"
+
+echo "$GNUPLOTCMD" | gnuplot > "$OUTPUTFILE"