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https://github.com/galaxyproject/galaxy.git
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Guruprasad Anada
95 lines
2.9 KiB
Bash
Executable File
95 lines
2.9 KiB
Bash
Executable File
#!/bin/sh
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# Modified fastq_quality_boxplot_graph.sh from FASTX-toolkit - FASTA/FASTQ preprocessing tools.
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# Copyright (C) 2009 A. Gordon (gordon@cshl.edu)
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#
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# This program is free software: you can redistribute it and/or modify
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# it under the terms of the GNU Affero General Public License as
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# published by the Free Software Foundation, either version 3 of the
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# License, or (at your option) any later version.
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#
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# This program is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU Affero General Public License for more details.
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#
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# You should have received a copy of the GNU Affero General Public License
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# along with this program. If not, see <http://www.gnu.org/licenses/>.
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function usage()
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{
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echo "SOLiD-Quality BoxPlot plotter"
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echo "Generates a SOLiD quality score box-plot graph "
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echo
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echo "Usage: $0 [-i INPUT.TXT] [-t TITLE] [-p] [-o OUTPUT]"
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echo
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echo " [-p] - Generate PostScript (.PS) file. Default is PNG image."
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echo " [-i INPUT.TXT] - Input file. Should be the output of \"solid_qual_stats\" program."
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echo " [-o OUTPUT] - Output file name. default is STDOUT."
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echo " [-t TITLE] - Title (usually the solid file name) - will be plotted on the graph."
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echo
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exit
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}
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#
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# Input Data columns: #pos cnt min max sum mean Q1 med Q3 IQR lW rW
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# As produced by "solid_qual_stats" program
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TITLE="" # default title is empty
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FILENAME=""
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OUTPUTTERM="set term png size 800,600"
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OUTPUTFILE="/dev/stdout" # Default output file is simply "stdout"
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while getopts ":t:i:o:ph" Option
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do
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case $Option in
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# w ) CMD=$OPTARG; FILENAME="PIMSLogList.txt"; TARGET="logfiles"; ;;
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t ) TITLE="for $OPTARG" ;;
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i ) FILENAME=$OPTARG ;;
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o ) OUTPUTFILE="$OPTARG" ;;
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p ) OUTPUTTERM="set term postscript enhanced color \"Helvetica\" 4" ;;
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h ) usage ;;
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* ) echo "unrecognized argument. use '-h' for usage information."; exit -1 ;;
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esac
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done
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shift $(($OPTIND - 1))
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if [ "$FILENAME" == "" ]; then
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usage
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fi
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if [ ! -r "$FILENAME" ]; then
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echo "Error: can't open input file ($1)." >&2
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exit 1
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fi
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#Read number of cycles from the stats file (each line is a cycle, minus the header line)
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#But for the graph, I want xrange to reach (num_cycles+1), so I don't subtract 1 now.
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NUM_CYCLES=$(cat "$FILENAME" | wc -l)
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GNUPLOTCMD="
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$OUTPUTTERM
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set boxwidth 0.8
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set size 1,1
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set key Left inside
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set xlabel \"read position\"
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set ylabel \"Quality Score \"
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set title \"Quality Scores $TITLE\"
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#set auto x
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set bars 4.0
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set xrange [ 0: $NUM_CYCLES ]
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set yrange [-2:45]
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set y2range [-2:45]
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set xtics 1
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set x2tics 1
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set ytics 2
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set y2tics 2
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set tics out
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set grid ytics
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set style fill empty
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plot '$FILENAME' using 1:7:11:12:9 with candlesticks lt 1 lw 1 title 'Quartiles' whiskerbars, \
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'' using 1:8:8:8:8 with candlesticks lt -1 lw 2 title 'Medians'
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"
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echo "$GNUPLOTCMD" | gnuplot > "$OUTPUTFILE"
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