Mercurial > repos > mvdbeek > scatterplot_test

comparison scatterplot.py @ 0:11627baf830e draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit a697f2f6d8562012634b3d63572c358b71ebf823-dirty
author mvdbeek
date Wed, 14 Sep 2016 12:40:20 -0400
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children b4102b163488
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-1:000000000000 0:11627baf830e
1 #!/usr/bin/env python
2 # Greg Von Kuster
3
4 import sys
5
6 from numpy import array
7 from rpy import r
8
9
10 def stop_err(msg):
11 sys.stderr.write(msg)
12 sys.exit()
13
14
15 def main():
16
17 in_fname = sys.argv[1]
18 out_fname = sys.argv[2]
19 try:
20 columns = int( sys.argv[3] ) - 1, int( sys.argv[4] ) - 1
21 except:
22 stop_err( "Columns not specified, your query does not contain a column of numerical data." )
23 title = sys.argv[5]
24 xlab = sys.argv[6]
25 ylab = sys.argv[7]
26
27 matrix = []
28 skipped_lines = 0
29 first_invalid_line = 0
30 invalid_value = ''
31 invalid_column = 0
32 i = 0
33 for i, line in enumerate( file( in_fname ) ):
34 valid = True
35 line = line.rstrip( '\r\n' )
36 if line and not line.startswith( '#' ):
37 row = []
38 fields = line.split( "\t" )
39 for column in columns:
40 try:
41 val = fields[column]
42 if val.lower() == "na":
43 row.append( float( "nan" ) )
44 else:
45 row.append( float( fields[column] ) )
46 except:
47 valid = False
48 skipped_lines += 1
49 if not first_invalid_line:
50 first_invalid_line = i + 1
51 try:
52 invalid_value = fields[column]
53 except:
54 invalid_value = ''
55 invalid_column = column + 1
56 break
57 else:
58 valid = False
59 skipped_lines += 1
60 if not first_invalid_line:
61 first_invalid_line = i + 1
62
63 if valid:
64 matrix.append( row )
65
66 if skipped_lines < i:
67 try:
68 r.pdf( out_fname, 8, 8 )
69 r.plot( array( matrix ), type="p", main=title, xlab=xlab, ylab=ylab, col="blue", pch=19 )
70 r.dev_off()
71 except Exception, exc:
72 stop_err( "%s" % str( exc ) )
73 else:
74 stop_err( "All values in both columns %s and %s are non-numeric or empty." % ( sys.argv[3], sys.argv[4] ) )
75
76 print "Scatter plot on columns %s, %s. " % ( sys.argv[3], sys.argv[4] )
77 if skipped_lines > 0:
78 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 )
79
80 r.quit( save="no" )
81
82 if __name__ == "__main__":
83 main()