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view fastx_toolkit-0.0.6/scripts/fastx_nucleotide_distribution_graph.sh @ 3:997f5136985f draft default tip
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author | xilinxu |
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date | Thu, 14 Aug 2014 04:52:17 -0400 |
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#!/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/>. usage() { echo "FASTA/Q Nucleotide Distribution Plotter" 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 \"fastx_quality_statistics\" program." echo " [-o OUTPUT] - Output file name. default is STDOUT." echo " [-t TITLE] - Title - 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 "fastq_quality_statistics" program TITLE="" # default title is empty FILENAME="" OUTPUTTERM="set term png size 1048,768" # 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 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 [ -z "$FILENAME" ]; then usage fi if [ ! -r "$FILENAME" ]; then echo "Error: can't open input file ($1)." >&2 exit 1 fi GNUPLOTCMD=" $OUTPUTTERM set boxwidth 0.75 absolute set size 1,1 set style fill solid 1.00 border -1 set xlabel \"read position\" set title \"Nucleotides distribution $TITLE\" set ylabel \"% of total (per read position)\" #set grid noxtics nomxtics ytics nomytics noztics nomztics \ # nox2tics nomx2tics noy2tics nomy2tics nocbtics nomcbtics #set grid layerdefault linetype 0 linewidth 1.000, linetype 0 linewidth 1.000 set key outside right top vertical Left reverse enhanced autotitles columnhead nobox set key invert samplen 4 spacing 1 width 0 height 0 set style histogram rowstacked set style data histograms set noytics set xtics 1 set yrange [ 0.00000 : 100.000 ] noreverse nowriteback plot '$FILENAME' using (100.*column(13)/column(18)):xtic(1) title \"A\" lt rgb \"#5050ff\", \ '' using (100.*column(14)/column(18)) title \"C\" lt rgb \"#e00000\", \ '' using (100.*column(15)/column(18)) title \"G\" lt rgb \"#00c000\", \ '' using (100.*column(16)/column(18)) title \"T\" lt rgb \"#e6e600\", \ '' using (100.*column(17)/column(18)) title \"N\" lt rgb \"pink\" " echo "$GNUPLOTCMD" | gnuplot > "$OUTPUTFILE"