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1 #!/usr/bin/env python
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2 #Greg Von Kuster
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3
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4 import sys
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5 from rpy import *
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6
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7 assert sys.version_info[:2] >= ( 2, 4 )
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8
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9 def stop_err(msg):
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10 sys.stderr.write(msg)
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11 sys.exit()
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12
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13 def main():
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14
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15 # Handle input params
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16 in_fname = sys.argv[1]
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17 out_fname = sys.argv[2]
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18 try:
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19 column = int( sys.argv[3] ) - 1
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20 except:
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21 stop_err( "Column not specified, your query does not contain a column of numerical data." )
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22 title = sys.argv[4]
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23 xlab = sys.argv[5]
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24 breaks = int( sys.argv[6] )
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25 if breaks == 0:
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26 breaks = "Sturges"
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27 if sys.argv[7] == "true":
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28 density = True
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29 else: density = False
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30 if len( sys.argv ) >= 9 and sys.argv[8] == "true":
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31 frequency = True
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32 else: frequency = False
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33
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34 matrix = []
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35 skipped_lines = 0
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36 first_invalid_line = 0
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37 invalid_value = ''
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38 i = 0
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39 for i, line in enumerate( file( in_fname ) ):
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40 valid = True
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41 line = line.rstrip('\r\n')
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42 # Skip comments
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43 if line and not line.startswith( '#' ):
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44 # Extract values and convert to floats
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45 row = []
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46 try:
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47 fields = line.split( "\t" )
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48 val = fields[column]
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49 if val.lower() == "na":
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50 row.append( float( "nan" ) )
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51 except:
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52 valid = False
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53 skipped_lines += 1
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54 if not first_invalid_line:
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55 first_invalid_line = i+1
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56 else:
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57 try:
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58 row.append( float( val ) )
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59 except ValueError:
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60 valid = False
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61 skipped_lines += 1
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62 if not first_invalid_line:
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63 first_invalid_line = i+1
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64 invalid_value = fields[column]
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65 else:
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66 valid = False
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67 skipped_lines += 1
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68 if not first_invalid_line:
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69 first_invalid_line = i+1
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70
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71 if valid:
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72 matrix += row
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73
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74 if skipped_lines < i:
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75 try:
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76 a = r.array( matrix )
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77 r.pdf( out_fname, 8, 8 )
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78 histogram = r.hist( a, probability=not frequency, main=title, xlab=xlab, breaks=breaks )
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79 if density:
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80 density = r.density( a )
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81 if frequency:
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82 scale_factor = len( matrix ) * ( histogram['mids'][1] - histogram['mids'][0] ) #uniform bandwidth taken from first 2 midpoints
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83 density[ 'y' ] = map( lambda x: x * scale_factor, density[ 'y' ] )
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84 r.lines( density )
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85 r.dev_off()
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86 except Exception, exc:
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87 stop_err( "%s" %str( exc ) )
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88 else:
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89 if i == 0:
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90 stop_err("Input dataset is empty.")
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91 else:
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92 stop_err( "All values in column %s are non-numeric." %sys.argv[3] )
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93
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94 print "Histogram of column %s. " %sys.argv[3]
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95 if skipped_lines > 0:
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96 print "Skipped %d invalid lines starting with line #%d, '%s'." % ( skipped_lines, first_invalid_line, invalid_value )
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97
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98 r.quit( save="no" )
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99
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100 if __name__ == "__main__":
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101 main()
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