[2] | 1 | #!/bin/sh |
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| 2 | |
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| 3 | # Modified fastq_quality_boxplot_graph.sh from FASTX-toolkit - FASTA/FASTQ preprocessing tools. |
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| 4 | # Copyright (C) 2009 A. Gordon (gordon@cshl.edu) |
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| 5 | # |
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| 6 | # This program is free software: you can redistribute it and/or modify |
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| 7 | # it under the terms of the GNU Affero General Public License as |
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| 8 | # published by the Free Software Foundation, either version 3 of the |
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| 9 | # License, or (at your option) any later version. |
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| 10 | # |
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| 11 | # This program is distributed in the hope that it will be useful, |
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| 12 | # but WITHOUT ANY WARRANTY; without even the implied warranty of |
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| 13 | # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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| 14 | # GNU Affero General Public License for more details. |
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| 15 | # |
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| 16 | # You should have received a copy of the GNU Affero General Public License |
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| 17 | # along with this program. If not, see <http://www.gnu.org/licenses/>. |
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| 18 | |
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| 19 | function usage() |
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| 20 | { |
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| 21 | echo "SOLiD-Quality BoxPlot plotter" |
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| 22 | echo "Generates a SOLiD quality score box-plot graph " |
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| 23 | echo |
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| 24 | echo "Usage: $0 [-i INPUT.TXT] [-t TITLE] [-p] [-o OUTPUT]" |
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| 25 | echo |
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| 26 | echo " [-p] - Generate PostScript (.PS) file. Default is PNG image." |
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| 27 | echo " [-i INPUT.TXT] - Input file. Should be the output of \"solid_qual_stats\" program." |
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| 28 | echo " [-o OUTPUT] - Output file name. default is STDOUT." |
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| 29 | echo " [-t TITLE] - Title (usually the solid file name) - will be plotted on the graph." |
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| 30 | echo |
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| 31 | exit |
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| 32 | } |
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| 33 | |
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| 34 | # |
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| 35 | # Input Data columns: #pos cnt min max sum mean Q1 med Q3 IQR lW rW |
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| 36 | # As produced by "solid_qual_stats" program |
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| 37 | |
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| 38 | TITLE="" # default title is empty |
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| 39 | FILENAME="" |
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| 40 | OUTPUTTERM="set term png size 800,600" |
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| 41 | OUTPUTFILE="/dev/stdout" # Default output file is simply "stdout" |
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| 42 | while getopts ":t:i:o:ph" Option |
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| 43 | do |
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| 44 | case $Option in |
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| 45 | # w ) CMD=$OPTARG; FILENAME="PIMSLogList.txt"; TARGET="logfiles"; ;; |
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| 46 | t ) TITLE="for $OPTARG" ;; |
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| 47 | i ) FILENAME=$OPTARG ;; |
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| 48 | o ) OUTPUTFILE="$OPTARG" ;; |
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| 49 | p ) OUTPUTTERM="set term postscript enhanced color \"Helvetica\" 4" ;; |
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| 50 | h ) usage ;; |
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| 51 | * ) echo "unrecognized argument. use '-h' for usage information."; exit -1 ;; |
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| 52 | esac |
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| 53 | done |
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| 54 | shift $(($OPTIND - 1)) |
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| 55 | |
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| 56 | |
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| 57 | if [ "$FILENAME" == "" ]; then |
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| 58 | usage |
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| 59 | fi |
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| 60 | |
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| 61 | if [ ! -r "$FILENAME" ]; then |
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| 62 | echo "Error: can't open input file ($1)." >&2 |
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| 63 | exit 1 |
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| 64 | fi |
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| 65 | |
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| 66 | #Read number of cycles from the stats file (each line is a cycle, minus the header line) |
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| 67 | #But for the graph, I want xrange to reach (num_cycles+1), so I don't subtract 1 now. |
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| 68 | NUM_CYCLES=$(cat "$FILENAME" | wc -l) |
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| 69 | |
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| 70 | GNUPLOTCMD=" |
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| 71 | $OUTPUTTERM |
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| 72 | set boxwidth 0.8 |
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| 73 | set size 1,1 |
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| 74 | set key Left inside |
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| 75 | set xlabel \"read position\" |
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| 76 | set ylabel \"Quality Score \" |
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| 77 | set title \"Quality Scores $TITLE\" |
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| 78 | #set auto x |
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| 79 | set bars 4.0 |
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| 80 | set xrange [ 0: $NUM_CYCLES ] |
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| 81 | set yrange [-2:45] |
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| 82 | set y2range [-2:45] |
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| 83 | set xtics 1 |
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| 84 | set x2tics 1 |
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| 85 | set ytics 2 |
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| 86 | set y2tics 2 |
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| 87 | set tics out |
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| 88 | set grid ytics |
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| 89 | set style fill empty |
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| 90 | plot '$FILENAME' using 1:7:11:12:9 with candlesticks lt 1 lw 1 title 'Quartiles' whiskerbars, \ |
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| 91 | '' using 1:8:8:8:8 with candlesticks lt -1 lw 2 title 'Medians' |
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| 92 | " |
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| 93 | |
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| 94 | echo "$GNUPLOTCMD" | gnuplot > "$OUTPUTFILE" |
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