root/galaxy-central/tools/stats/gsummary.py

リビジョン 2, 4.5 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

  • 属性 svn:executable の設定値 *
行番号 
1#!/usr/bin/env python
2
3import sys, re, tempfile
4from rpy import *
5# Older py compatibility
6try:
7    set()
8except:
9    from sets import Set as set
10
11assert sys.version_info[:2] >= ( 2, 4 )
12
13def stop_err( msg ):
14    sys.stderr.write( msg )
15    sys.exit()
16
17def 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
26def 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        set_default_mode( NO_CONVERSION )
95        r_data_frame = r.read_table( tmp_file.name, header=True, sep="\t" )
96       
97        outfile = open( outfile_name, 'w' )
98
99        for col in re.compile( 'c[0-9]+' ).findall( expression ):
100            r.assign( col, r[ "$" ]( r_data_frame, col ) )
101        try:
102            summary = summary_func( r( expression ) )
103        except RException, s:
104            outfile.close()
105            stop_err( "Computation resulted in the following error: %s" % str( s ) )
106        summary = summary.as_py( BASIC_CONVERSION )
107        outfile.write( "#%s\n" % headings_str )
108        outfile.write( "%s\n" % "\t".join( [ "%g" % ( summary[ k ] ) for k in headings ] ) )
109        outfile.close()
110
111        if skipped_lines:
112            print "Skipped %d invalid lines beginning with line #%d.  See tool tips for data requirements." % ( skipped_lines, first_invalid_line )       
113
114if __name__ == "__main__": main()
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