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144 lines
4.8 KiB
Python
144 lines
4.8 KiB
Python
#!/usr/bin/env python2.4
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"""
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histogram_gnuplot.py <datafile> <xtic column> <column_list> <title> <ylabel> <yrange_min> <yrange_max> <grath_file>
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a generic histogram builder based on gnuplot backend
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data_file - tab delimited file with data
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xtic_column - column containing labels for x ticks [integer, 0 means no ticks]
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column_list - comma separated list of columns to plot
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title - title for the entire histrogram
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ylabel - y axis label
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yrange_max - minimal value at the y axis (integer)
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yrange_max - maximal value at the y_axis (integer)
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to set yrange to autoscaling assign 0 to yrange_min and yrange_max
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graph_file - file to write histogram image to
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pdf_size - as X,Y pair in inches (e.g., 11,8 or 8,11 etc.)
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This tool required gnuplot and gnuplot.py
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anton nekrutenko | anton@bx.psu.edu
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"""
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from Numeric import *
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import Gnuplot, Gnuplot.funcutils
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import sys, string, tempfile, os
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def stop_err(msg):
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sys.stderr.write(msg)
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sys.exit()
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def main(tmpFileName):
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skipped_lines_count = 0
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skipped_lines_index = []
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gf = open(tmpFileName, 'w')
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try:
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in_file = open( sys.argv[1], 'r' )
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xtic = int( sys.argv[2] )
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col_list = string.split( sys.argv[3],"," )
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title = 'set title "' + sys.argv[4] + '"'
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ylabel = 'set ylabel "' + sys.argv[5] + '"'
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ymin = sys.argv[6]
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ymax = sys.argv[7]
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img_file = sys.argv[8]
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pdf_size = sys.argv[9]
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except:
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stop_err("Check arguments\n")
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try:
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int( col_list[0] )
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except:
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stop_err('You forgot to set columns for plotting\n')
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for i, line in enumerate( in_file ):
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valid = True
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line = line.rstrip('\r\n')
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if line and not line.startswith( '#' ):
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row = []
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try:
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fields = line.split( '\t' )
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for col in col_list:
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row.append( str( float( fields[int( col )-1] ) ) )
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except:
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valid = False
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skipped_lines_count += 1
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skipped_lines_index.append(i)
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else:
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valid = False
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skipped_lines_count += 1
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skipped_lines_index.append(i)
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if valid and xtic > 0:
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row.append( fields[xtic-1] )
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elif valid and xtic == 0:
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row.append( str( i ) )
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if valid:
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gf.write( '\t'.join( row ) )
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gf.write( '\n' )
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if skipped_lines_count < i:
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#prepare 'using' clause of plot statement
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g_plot_command = ' ';
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#set the first column
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if xtic > 0:
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g_plot_command = "'%s' using 1:xticlabels(%s) ti 'Column %s', " % ( tmpFileName, str( len( row ) ), col_list[0] )
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else:
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g_plot_command = "'%s' using 1 ti 'Column %s', " % ( tmpFileName, col_list[0] )
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#set subsequent columns
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for i in range(1,len(col_list)):
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g_plot_command += "'%s' using %s t 'Column %s', " % ( tmpFileName, str( i+1 ), col_list[i] )
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g_plot_command = g_plot_command.rstrip( ', ' )
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yrange = 'set yrange [' + ymin + ":" + ymax + ']'
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try:
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g = Gnuplot.Gnuplot()
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g('reset')
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g('set boxwidth 0.9 absolute')
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g('set style fill solid 1.00 border -1')
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g('set style histogram clustered gap 5 title offset character 0, 0, 0')
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g('set xtics border in scale 1,0.5 nomirror rotate by 90 offset character 0, 0, 0')
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g('set key invert reverse Left outside')
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if xtic == 0: g('unset xtics')
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g(title)
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g(ylabel)
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g_term = 'set terminal pdf size ' + pdf_size
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g(g_term)
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g_out = 'set output "' + img_file + '"'
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if ymin != ymax:
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g(yrange)
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g(g_out)
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g('set style data histograms')
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g.plot(g_plot_command)
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except:
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stop_err("Gnuplot error: Data cannot be plotted")
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else:
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sys.stderr.write('Column(s) %s of your dataset do not contain valid numeric data' %sys.argv[3] )
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if skipped_lines_count > 0:
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sys.stdout.write('\nWARNING. You dataset contain(s) %d invalid lines starting with line #%d. These lines were skipped while building the graph.\n' % ( skipped_lines_count, skipped_lines_index[0]+1 ) )
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if __name__ == "__main__":
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# The tempfile initialization is here because while inside the main() it seems to create a condition
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# when the file is removed before gnuplot has a chance of accessing it
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gp_data_file = tempfile.NamedTemporaryFile('w')
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main(gp_data_file.name)
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