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1 #!/bin/sh
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2
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3 # 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 usage()
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20 {
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21 echo "FASTA/Q Nucleotide Distribution Plotter"
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22 echo
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23 echo "Usage: $0 [-i INPUT.TXT] [-t TITLE] [-p] [-o OUTPUT]"
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24 echo
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25 echo " [-p] - Generate PostScript (.PS) file. Default is PNG image."
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26 echo " [-i INPUT.TXT] - Input file. Should be the output of \"fastx_quality_statistics\" program."
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27 echo " [-o OUTPUT] - Output file name. default is STDOUT."
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28 echo " [-t TITLE] - Title - will be plotted on the graph."
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29 echo
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30 exit
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31 }
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32
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33 #
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34 # 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
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35 # As produced by "fastq_quality_statistics" program
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36
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37 TITLE="" # default title is empty
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38 FILENAME=""
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39 OUTPUTTERM="set term png size 1048,768" # default output terminal is "PNG"
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40 OUTPUTFILE="/dev/stdout" # Default output file is simply "stdout"
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41 while getopts ":t:i:o:ph" Option
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42 do
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43 case $Option in
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44 t ) TITLE="for $OPTARG" ;;
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45 i ) FILENAME=$OPTARG ;;
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46 o ) OUTPUTFILE="$OPTARG" ;;
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47 p ) OUTPUTTERM="set term postscript enhanced color \"Helvetica\" 8" ;;
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48 h ) usage ;;
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49 * ) echo "unrecognized argument. use '-h' for usage information."; exit -1 ;;
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50 esac
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51 done
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52 shift $(($OPTIND - 1))
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53
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54
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55 if [ -z "$FILENAME" ]; then
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56 usage
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57 fi
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58
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59 if [ ! -r "$FILENAME" ]; then
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60 echo "Error: can't open input file ($1)." >&2
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61 exit 1
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62 fi
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63
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64 GNUPLOTCMD="
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65 $OUTPUTTERM
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66 set boxwidth 0.75 absolute
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67 set size 1,1
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68 set style fill solid 1.00 border -1
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69 set xlabel \"read position\"
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70 set title \"Nucleotides distribution $TITLE\"
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71 set ylabel \"% of total (per read position)\"
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72 #set grid noxtics nomxtics ytics nomytics noztics nomztics \
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73 # nox2tics nomx2tics noy2tics nomy2tics nocbtics nomcbtics
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74 #set grid layerdefault linetype 0 linewidth 1.000, linetype 0 linewidth 1.000
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75 set key outside right top vertical Left reverse enhanced autotitles columnhead nobox
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76 set key invert samplen 4 spacing 1 width 0 height 0
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77 set style histogram rowstacked
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78 set style data histograms
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79 set noytics
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80 set xtics 1
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81 set yrange [ 0.00000 : 100.000 ] noreverse nowriteback
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82
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83 plot '$FILENAME' using (100.*column(13)/column(18)):xtic(1) title \"A\" lt rgb \"#5050ff\", \
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84 '' using (100.*column(14)/column(18)) title \"C\" lt rgb \"#e00000\", \
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85 '' using (100.*column(15)/column(18)) title \"G\" lt rgb \"#00c000\", \
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86 '' using (100.*column(16)/column(18)) title \"T\" lt rgb \"#e6e600\", \
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87 '' using (100.*column(17)/column(18)) title \"N\" lt rgb \"pink\"
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88 "
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89
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90 echo "$GNUPLOTCMD" | gnuplot > "$OUTPUTFILE"
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