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https://github.com/galaxyproject/galaxy.git
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James Taylor
88 lines
2.2 KiB
Python
88 lines
2.2 KiB
Python
#!/usr/bin/env python2.4
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# python histogram input_file output_file column bins
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import sys, os
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import matplotlib; matplotlib.use('Agg')
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from pylab import *
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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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if __name__ == '__main__':
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# parse the arguments
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if len(sys.argv) != 6:
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stop_err('Usage: python histogram.py input_file column bins output_file style')
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sys.exit()
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mode = sys.argv[5]
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HIST = mode == 'hist'
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try:
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col = int(float(sys.argv[2]))
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if HIST:
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bin = int(float(sys.argv[3]))
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else:
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# hack, this parameter is the plotting style for scatter plots
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if sys.argv[3] == 'P':
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style = 'o'
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elif sys.argv[3] == 'LP':
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style = 'o-'
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else:
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style = '-'
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except:
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msg = 'Parameter were not numbers %s, %s' % (sys.argv[3], sys.argv[4])
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stop_err(msg)
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# validate arguments
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inp_file = sys.argv[1]
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out_file = sys.argv[4]
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if HIST:
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print "Histogram on column %s (%s bins)" % (col, bin)
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else:
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print "Scatterplot on column %s" % (col)
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xcol= col -1
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# read the file
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values = []
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try:
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count = 0
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for line in file(inp_file):
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count += 1
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line = line.strip()
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if line and line[0] != '#':
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values.append(float(line.split()[xcol]))
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except Exception, e:
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stop_err('%s' % e)
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stop_err("Non numerical data at line %d, column %d" % (count, col) )
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# plot the data
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if HIST:
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n, bins, patches = hist(values, bins=bin, normed=0)
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else:
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plot(values, style)
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xlabel('values')
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ylabel('counts')
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if HIST:
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title('Histogram of values over column %s (%s bins)' % (col, len(bins)) )
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else:
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title('Scatterplot over column %s' % col )
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grid(True)
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# the plotter detects types by file extension
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png_out = out_file + '.png' # force it to png
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savefig(png_out)
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# shuffle it back and clean up
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data = file(png_out, 'rb').read()
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fp = open(out_file, 'wb')
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fp.write(data)
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fp.close()
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os.remove(png_out)
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