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comparison fastx_toolkit-0.0.6/scripts/fastx_nucleotide_distribution_graph.sh @ 3:997f5136985f draft default tip

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author xilinxu
date Thu, 14 Aug 2014 04:52:17 -0400
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2:dfe9332138cf 3:997f5136985f
1 #!/bin/sh
2
3 # FASTX-toolkit - FASTA/FASTQ preprocessing tools.
4 # Copyright (C) 2009 A. Gordon (gordon@cshl.edu)
5 #
6 # This program is free software: you can redistribute it and/or modify
7 # it under the terms of the GNU Affero General Public License as
8 # published by the Free Software Foundation, either version 3 of the
9 # License, or (at your option) any later version.
10 #
11 # This program is distributed in the hope that it will be useful,
12 # but WITHOUT ANY WARRANTY; without even the implied warranty of
13 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14 # GNU Affero General Public License for more details.
15 #
16 # You should have received a copy of the GNU Affero General Public License
17 # along with this program. If not, see <http://www.gnu.org/licenses/>.
18
19 usage()
20 {
21 echo "FASTA/Q Nucleotide Distribution Plotter"
22 echo
23 echo "Usage: $0 [-i INPUT.TXT] [-t TITLE] [-p] [-o OUTPUT]"
24 echo
25 echo " [-p] - Generate PostScript (.PS) file. Default is PNG image."
26 echo " [-i INPUT.TXT] - Input file. Should be the output of \"fastx_quality_statistics\" program."
27 echo " [-o OUTPUT] - Output file name. default is STDOUT."
28 echo " [-t TITLE] - Title - will be plotted on the graph."
29 echo
30 exit
31 }
32
33 #
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
35 # As produced by "fastq_quality_statistics" program
36
37 TITLE="" # default title is empty
38 FILENAME=""
39 OUTPUTTERM="set term png size 1048,768" # default output terminal is "PNG"
40 OUTPUTFILE="/dev/stdout" # Default output file is simply "stdout"
41 while getopts ":t:i:o:ph" Option
42 do
43 case $Option in
44 t ) TITLE="for $OPTARG" ;;
45 i ) FILENAME=$OPTARG ;;
46 o ) OUTPUTFILE="$OPTARG" ;;
47 p ) OUTPUTTERM="set term postscript enhanced color \"Helvetica\" 8" ;;
48 h ) usage ;;
49 * ) echo "unrecognized argument. use '-h' for usage information."; exit -1 ;;
50 esac
51 done
52 shift $(($OPTIND - 1))
53
54
55 if [ -z "$FILENAME" ]; then
56 usage
57 fi
58
59 if [ ! -r "$FILENAME" ]; then
60 echo "Error: can't open input file ($1)." >&2
61 exit 1
62 fi
63
64 GNUPLOTCMD="
65 $OUTPUTTERM
66 set boxwidth 0.75 absolute
67 set size 1,1
68 set style fill solid 1.00 border -1
69 set xlabel \"read position\"
70 set title \"Nucleotides distribution $TITLE\"
71 set ylabel \"% of total (per read position)\"
72 #set grid noxtics nomxtics ytics nomytics noztics nomztics \
73 # nox2tics nomx2tics noy2tics nomy2tics nocbtics nomcbtics
74 #set grid layerdefault linetype 0 linewidth 1.000, linetype 0 linewidth 1.000
75 set key outside right top vertical Left reverse enhanced autotitles columnhead nobox
76 set key invert samplen 4 spacing 1 width 0 height 0
77 set style histogram rowstacked
78 set style data histograms
79 set noytics
80 set xtics 1
81 set yrange [ 0.00000 : 100.000 ] noreverse nowriteback
82
83 plot '$FILENAME' using (100.*column(13)/column(18)):xtic(1) title \"A\" lt rgb \"#5050ff\", \
84 '' using (100.*column(14)/column(18)) title \"C\" lt rgb \"#e00000\", \
85 '' using (100.*column(15)/column(18)) title \"G\" lt rgb \"#00c000\", \
86 '' using (100.*column(16)/column(18)) title \"T\" lt rgb \"#e6e600\", \
87 '' using (100.*column(17)/column(18)) title \"N\" lt rgb \"pink\"
88 "
89
90 echo "$GNUPLOTCMD" | gnuplot > "$OUTPUTFILE"