Mercurial > repos > bgruening > upload_testing

comparison histogram.py @ 90:b061185bcb83 draft

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Uploaded
author bernhardlutz
date Thu, 23 Jan 2014 14:53:46 -0500
parents c4a3a8999945
children
comparison
equal deleted inserted replaced
89:71e953a4191d 90:b061185bcb83
1 #!/usr/bin/env python
2 #Greg Von Kuster
3
4 import sys
5 #from rpy import *
6 import rpy2.robjects as robjects
7 from rpy2.robjects.packages import importr
8 r = robjects.r
9 grdevices = importr('grDevices')
10
11
12 assert sys.version_info[:2] >= ( 2, 4 )
13
14 def stop_err(msg):
15 sys.stderr.write(msg)
16 sys.exit()
17
18 def main():
19
20 # Handle input params
21 in_fname = sys.argv[1]
22 out_fname = sys.argv[2]
23 try:
24 column = int( sys.argv[3] ) - 1
25 except:
26 stop_err( "Column not specified, your query does not contain a column of numerical data." )
27 title = sys.argv[4]
28 xlab = sys.argv[5]
29 breaks = int( sys.argv[6] )
30 if breaks == 0:
31 breaks = "Sturges"
32 if sys.argv[7] == "true":
33 density = True
34 else: density = False
35 if len( sys.argv ) >= 9 and sys.argv[8] == "true":
36 frequency = True
37 else: frequency = False
38
39 matrix = []
40 skipped_lines = 0
41 first_invalid_line = 0
42 invalid_value = ''
43 i = 0
44 for i, line in enumerate( file( in_fname ) ):
45 valid = True
46 line = line.rstrip('\r\n')
47 # Skip comments
48 if line and not line.startswith( '#' ):
49 # Extract values and convert to floats
50 row = []
51 try:
52 fields = line.split( "\t" )
53 val = fields[column]
54 if val.lower() == "na":
55 row.append( float( "nan" ) )
56 except:
57 valid = False
58 skipped_lines += 1
59 if not first_invalid_line:
60 first_invalid_line = i+1
61 else:
62 try:
63 row.append( float( val ) )
64 except ValueError:
65 valid = False
66 skipped_lines += 1
67 if not first_invalid_line:
68 first_invalid_line = i+1
69 invalid_value = fields[column]
70 else:
71 valid = False
72 skipped_lines += 1
73 if not first_invalid_line:
74 first_invalid_line = i+1
75
76 if valid:
77 matrix += row
78
79 if skipped_lines < i:
80 try:
81 #a = r.array( matrix )
82 fv = robjects.FloatVector(matrix)
83 a = r['matrix'](fv, ncol=1,byrow=True)
84 #r.pdf( out_fname, 8, 8 )
85 r.pdf( out_fname, 8, 8 )
86 histogram = r.hist( a, probability=not frequency, main=title, xlab=xlab, breaks=breaks )
87 if density:
88 density = r.density( a )
89 if frequency:
90 scale_factor = len( matrix ) * ( histogram['mids'][1] - histogram['mids'][0] ) #uniform bandwidth taken from first 2 midpoints
91 density[ 'y' ] = map( lambda x: x * scale_factor, density[ 'y' ] )
92 r.lines( density )
93 #r.dev_off()
94 grdevices.dev_off()
95 except Exception, exc:
96 stop_err( "%s" %str( exc ) )
97 else:
98 if i == 0:
99 stop_err("Input dataset is empty.")
100 else:
101 stop_err( "All values in column %s are non-numeric." %sys.argv[3] )
102
103 print "Histogram of column %s. " %sys.argv[3]
104 if skipped_lines > 0:
105 print "Skipped %d invalid lines starting with line #%d, '%s'." % ( skipped_lines, first_invalid_line, invalid_value )
106
107 #r.quit( save="no" )
108
109 if __name__ == "__main__":
110 main()