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