|
0
|
1 #!/usr/bin/env python
|
|
|
2 #Erno Lindfors
|
|
|
3
|
|
|
4 import sys
|
|
|
5 from rpy import *
|
|
|
6
|
|
|
7 def stop_err(msg):
|
|
|
8 sys.stderr.write(msg)
|
|
|
9 sys.exit()
|
|
|
10
|
|
|
11 def main():
|
|
|
12
|
|
|
13 in_fname = sys.argv[1]
|
|
|
14 out_fname = sys.argv[2]
|
|
|
15 try:
|
|
|
16 #columns = int( sys.argv[3] ) - 1, int( sys.argv[4] ) - 1
|
|
|
17 columns = int( sys.argv[3] ) - 1
|
|
|
18 except:
|
|
|
19 stop_err( "Columns not specified, your query does not contain a column of numerical data." )
|
|
|
20
|
|
|
21 matrix = []
|
|
|
22 skipped_lines = 0
|
|
|
23 first_invalid_line = 0
|
|
|
24 invalid_value = ''
|
|
|
25 invalid_column = 0
|
|
|
26 i = 0
|
|
|
27 for i, line in enumerate( file( in_fname ) ):
|
|
|
28 valid = True
|
|
|
29 line = line.rstrip( '\r\n' )
|
|
|
30 if line and not line.startswith( '#' ):
|
|
|
31 row = []
|
|
|
32 fields = line.split( "\t" )
|
|
|
33 for column in columns:
|
|
|
34 try:
|
|
|
35 val = fields[column]
|
|
|
36 if val.lower() == "na":
|
|
|
37 row.append( float( "nan" ) )
|
|
|
38 else:
|
|
|
39 row.append( float( fields[column] ) )
|
|
|
40 except:
|
|
|
41 valid = False
|
|
|
42 skipped_lines += 1
|
|
|
43 if not first_invalid_line:
|
|
|
44 first_invalid_line = i + 1
|
|
|
45 try:
|
|
|
46 invalid_value = fields[column]
|
|
|
47 except:
|
|
|
48 invalid_value = ''
|
|
|
49 invalid_column = column + 1
|
|
|
50 break
|
|
|
51 else:
|
|
|
52 valid = False
|
|
|
53 skipped_lines += 1
|
|
|
54 if not first_invalid_line:
|
|
|
55 first_invalid_line = i+1
|
|
|
56
|
|
|
57 if valid:
|
|
|
58 matrix.append( row )
|
|
|
59
|
|
|
60 if skipped_lines < i:
|
|
|
61 try:
|
|
|
62 #r.pdf( out_fname, 8, 8 )
|
|
|
63 #r.plot( array( matrix ), type="p", main=title, xlab=xlab, ylab=ylab, col="blue", pch=19 )
|
|
|
64 #r.dev_off()
|
|
|
65 r.sum(inputNumbers)
|
|
|
66 r.write.table(
|
|
|
67 sum(matrix[,1],
|
|
|
68 out_fname,
|
|
|
69 row.names = FALSE,
|
|
|
70 col.names = c("Sum"),
|
|
|
71 quote = FALSE
|
|
|
72 )
|
|
|
73 except Exception, exc:
|
|
|
74 stop_err( "%s" %str( exc ) )
|
|
|
75 else:
|
|
|
76 stop_err( "All values in column %s are non-numeric or empty." % (sys.argv[3]) )
|
|
|
77
|
|
|
78 print "Scatter plot on column %s. " % (sys.argv[3])
|
|
|
79 if skipped_lines > 0:
|
|
|
80 print "Skipped %d lines starting with line #%d, value '%s' in column %d is not numeric." % ( skipped_lines, first_invalid_line, invalid_value, invalid_column )
|
|
|
81
|
|
|
82 r.quit( save="no" )
|
|
|
83
|
|
|
84 if __name__ == "__main__":
|
|
|
85 main() |
