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comparison gsummary.py @ 80:c4a3a8999945 draft

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Uploaded
author bernhardlutz
date Mon, 20 Jan 2014 14:39:43 -0500
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79:dc82017052ac 80:c4a3a8999945
1 #!/usr/bin/env python
2
3 import sys
4 import re
5 import tempfile
6 #from rpy import *
7 import rpy2.robjects as robjects
8 r = robjects.r
9 from rpy2.robjects.vectors import DataFrame
10
11 assert sys.version_info[:2] >= ( 2, 4 )
12
13 def stop_err( msg ):
14 sys.stderr.write( msg )
15 sys.exit()
16
17 def S3_METHODS( all="key" ):
18 Group_Math = [ "abs", "sign", "sqrt", "floor", "ceiling", "trunc", "round", "signif",
19 "exp", "log", "cos", "sin", "tan", "acos", "asin", "atan", "cosh", "sinh", "tanh",
20 "acosh", "asinh", "atanh", "lgamma", "gamma", "gammaCody", "digamma", "trigamma",
21 "cumsum", "cumprod", "cummax", "cummin", "c" ]
22 Group_Ops = [ "+", "-", "*", "/", "^", "%%", "%/%", "&", "|", "!", "==", "!=", "<", "<=", ">=", ">", "(", ")", "~", "," ]
23 if all is "key":
24 return { 'Math' : Group_Math, 'Ops' : Group_Ops }
25
26 def main():
27 try:
28 datafile = sys.argv[1]
29 outfile_name = sys.argv[2]
30 expression = sys.argv[3]
31 except:
32 stop_err( 'Usage: python gsummary.py input_file ouput_file expression' )
33
34 math_allowed = S3_METHODS()[ 'Math' ]
35 ops_allowed = S3_METHODS()[ 'Ops' ]
36
37 # Check for invalid expressions
38 for word in re.compile( '[a-zA-Z]+' ).findall( expression ):
39 if word and not word in math_allowed:
40 stop_err( "Invalid expression '%s': term '%s' is not recognized or allowed" %( expression, word ) )
41 symbols = set()
42 for symbol in re.compile( '[^a-z0-9\s]+' ).findall( expression ):
43 if symbol and not symbol in ops_allowed:
44 stop_err( "Invalid expression '%s': operator '%s' is not recognized or allowed" % ( expression, symbol ) )
45 else:
46 symbols.add( symbol )
47 if len( symbols ) == 1 and ',' in symbols:
48 # User may have entered a comma-separated list r_data_frame columns
49 stop_err( "Invalid columns '%s': this tool requires a single column or expression" % expression )
50
51 # Find all column references in the expression
52 cols = []
53 for col in re.compile( 'c[0-9]+' ).findall( expression ):
54 try:
55 cols.append( int( col[1:] ) - 1 )
56 except:
57 pass
58
59 tmp_file = tempfile.NamedTemporaryFile( 'w+b' )
60 # Write the R header row to the temporary file
61 hdr_str = "\t".join( "c%s" % str( col+1 ) for col in cols )
62 tmp_file.write( "%s\n" % hdr_str )
63 skipped_lines = 0
64 first_invalid_line = 0
65 i = 0
66 for i, line in enumerate( file( datafile ) ):
67 line = line.rstrip( '\r\n' )
68 if line and not line.startswith( '#' ):
69 valid = True
70 fields = line.split( '\t' )
71 # Write the R data row to the temporary file
72 for col in cols:
73 try:
74 float( fields[ col ] )
75 except:
76 skipped_lines += 1
77 if not first_invalid_line:
78 first_invalid_line = i + 1
79 valid = False
80 break
81 if valid:
82 data_str = "\t".join( fields[ col ] for col in cols )
83 tmp_file.write( "%s\n" % data_str )
84 tmp_file.flush()
85
86 if skipped_lines == i + 1:
87 stop_err( "Invalid column or column data values invalid for computation. See tool tips and syntax for data requirements." )
88 else:
89 # summary function and return labels
90 summary_func = r( "function( x ) { c( sum=sum( as.numeric( x ), na.rm=T ), mean=mean( as.numeric( x ), na.rm=T ), stdev=sd( as.numeric( x ), na.rm=T ), quantile( as.numeric( x ), na.rm=TRUE ) ) }" )
91 headings = [ 'sum', 'mean', 'stdev', '0%', '25%', '50%', '75%', '100%' ]
92 headings_str = "\t".join( headings )
93
94 #r.set_default_mode( NO_CONVERSION )
95 #r_data_frame = r.read_table( tmp_file.name, header=True, sep="\t" )
96 r_data_frame = DataFrame.from_csvfile( tmp_file.name, header=True, sep="\t" )
97
98 outfile = open( outfile_name, 'w' )
99
100 for col in re.compile( 'c[0-9]+' ).findall( expression ):
101 r.assign( col, r[ "$" ]( r_data_frame, col ) )
102 try:
103 summary = summary_func( r( expression ) )
104 except RException, s:
105 outfile.close()
106 stop_err( "Computation resulted in the following error: %s" % str( s ) )
107 #summary = summary.as_py( BASIC_CONVERSION )
108 outfile.write( "#%s\n" % headings_str )
109 print summary
110 print summary.r_repr()
111 outfile.write( "%s\n" % "\t".join( [ "%g" % ( summary.rx2( k )[0] ) for k in headings ] ) )
112 outfile.close()
113
114 if skipped_lines:
115 print "Skipped %d invalid lines beginning with line #%d. See tool tips for data requirements." % ( skipped_lines, first_invalid_line )
116
117 if __name__ == "__main__": main()