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92 lines
2.5 KiB
Python
92 lines
2.5 KiB
Python
#!/usr/bin/env python
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#Greg Von Kuster
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import sys
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from rpy import *
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assert sys.version_info[:2] >= ( 2, 4 )
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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():
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# Handle input params
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in_fname = sys.argv[1]
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out_fname = sys.argv[2]
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try:
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column = int( sys.argv[3] ) - 1
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except:
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stop_err( "Column not specified, your query does not contain a column of numerical data." )
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title = sys.argv[4]
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xlab = sys.argv[5]
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breaks = int( sys.argv[6] )
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if breaks == 0:
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breaks = "Sturges"
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if sys.argv[7] == "true":
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density = True
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else: density = False
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matrix = []
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skipped_lines = 0
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first_invalid_line = 0
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invalid_value = ''
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for i, line in enumerate( file( in_fname ) ):
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valid = True
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line = line.rstrip('\r\n')
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# Skip comments
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if line and not line.startswith( '#' ):
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# Extract values and convert to floats
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row = []
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try:
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fields = line.split( "\t" )
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val = fields[column]
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if val.lower() == "na":
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row.append( float( "nan" ) )
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except:
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valid = False
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skipped_lines += 1
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if not first_invalid_line:
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first_invalid_line = i+1
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else:
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try:
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row.append( float( val ) )
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except ValueError:
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valid = False
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skipped_lines += 1
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if not first_invalid_line:
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first_invalid_line = i+1
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invalid_value = fields[column]
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else:
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valid = False
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skipped_lines += 1
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if not first_invalid_line:
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first_invalid_line = i+1
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if valid:
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matrix.append( row )
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if skipped_lines < i:
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try:
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a = array( matrix )
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r.pdf( out_fname, 8, 8 )
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r.hist( a, probability=True, main=title, xlab=xlab, breaks=breaks )
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if density:
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r.lines( r.density( a ) )
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r.dev_off()
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except Exception, exc:
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stop_err( "%s" %str( exc ) )
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else:
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stop_err( "All values in column %s are non-numeric." %sys.argv[3] )
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print "Histogram of column %s. " %sys.argv[3]
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if skipped_lines > 0:
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print "Skipped %d invalid lines starting with line #%d, '%s'." % ( skipped_lines, first_invalid_line, invalid_value )
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r.quit( save="no" )
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if __name__ == "__main__":
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main()
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