Mercurial > repos > xuebing > sharplabtool

comparison tools/stats/column_maker.py @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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-1:000000000000 0:9071e359b9a3
1 #!/usr/bin/env python
2 # This tool takes a tab-delimited textfile as input and creates another column in the file which is the result of
3 # a computation performed on every row in the original file. The tool will skip over invalid lines within the file,
4 # informing the user about the number of lines skipped.
5 import sys, re, os.path
6 from galaxy import eggs
7 from galaxy.tools import validation
8 from galaxy.datatypes import metadata
9 from math import log,exp,sqrt,ceil,floor
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 inp_file = sys.argv[1]
18 out_file = sys.argv[2]
19 expr = sys.argv[3]
20 round_result = sys.argv[4]
21 try:
22 in_columns = int( sys.argv[5] )
23 except:
24 stop_err( "Missing or invalid 'columns' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it. This tool can only be used with tab-delimited data." )
25 if in_columns < 2:
26 # To be considered tabular, data must fulfill requirements of the sniff.is_column_based() method.
27 stop_err( "Missing or invalid 'columns' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it. This tool can only be used with tab-delimited data." )
28 try:
29 in_column_types = sys.argv[6].split( ',' )
30 except:
31 stop_err( "Missing or invalid 'column_types' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it. This tool can only be used with tab-delimited data." )
32 if len( in_column_types ) != in_columns:
33 stop_err( "The 'columns' metadata setting does not conform to the 'column_types' metadata setting, click the pencil icon in the history item and select the Auto-detect option to correct it. This tool can only be used with tab-delimited data." )
34
35 # Unescape if input has been escaped
36 mapped_str = {
37 '__lt__': '<',
38 '__le__': '<=',
39 '__eq__': '==',
40 '__ne__': '!=',
41 '__gt__': '>',
42 '__ge__': '>=',
43 '__sq__': '\'',
44 '__dq__': '"',
45 }
46 for key, value in mapped_str.items():
47 expr = expr.replace( key, value )
48
49 # Prepare the column variable names and wrappers for column data types
50 cols, type_casts = [], []
51 for col in range( 1, in_columns + 1 ):
52 col_name = "c%d" % col
53 cols.append( col_name )
54 col_type = in_column_types[ col - 1 ].strip()
55 if round_result == 'no' and col_type == 'int':
56 col_type = 'float'
57 type_cast = "%s(%s)" % ( col_type, col_name )
58 type_casts.append( type_cast )
59
60 col_str = ', '.join( cols ) # 'c1, c2, c3, c4'
61 type_cast_str = ', '.join( type_casts ) # 'str(c1), int(c2), int(c3), str(c4)'
62 assign = "%s = line.split( '\\t' )" % col_str
63 wrap = "%s = %s" % ( col_str, type_cast_str )
64 skipped_lines = 0
65 first_invalid_line = 0
66 invalid_line = None
67 lines_kept = 0
68 total_lines = 0
69 out = open( out_file, 'wt' )
70
71 # Read input file, skipping invalid lines, and perform computation that will result in a new column
72 code = '''
73 for i, line in enumerate( file( inp_file ) ):
74 total_lines += 1
75 line = line.rstrip( '\\r\\n' )
76 if not line or line.startswith( '#' ):
77 skipped_lines += 1
78 if not invalid_line:
79 first_invalid_line = i + 1
80 invalid_line = line
81 continue
82 try:
83 %s
84 %s
85 new_val = %s
86 if round_result == "yes":
87 new_val = int( round( new_val ) )
88 new_line = line + '\\t' + str( new_val )
89 print >> out, new_line
90 lines_kept += 1
91 except:
92 skipped_lines += 1
93 if not invalid_line:
94 first_invalid_line = i + 1
95 invalid_line = line
96 ''' % ( assign, wrap, expr )
97
98 valid_expr = True
99 try:
100 exec code
101 except Exception, e:
102 out.close()
103 if str( e ).startswith( 'invalid syntax' ):
104 valid_expr = False
105 stop_err( 'Expression "%s" likely invalid. See tool tips, syntax and examples.' % expr )
106 else:
107 stop_err( str( e ) )
108
109 if valid_expr:
110 out.close()
111 valid_lines = total_lines - skipped_lines
112 print 'Creating column %d with expression %s' % ( in_columns + 1, expr )
113 if valid_lines > 0:
114 print 'kept %4.2f%% of %d lines.' % ( 100.0*lines_kept/valid_lines, total_lines )
115 else:
116 print 'Possible invalid expression "%s" or non-existent column referenced. See tool tips, syntax and examples.' % expr
117 if skipped_lines > 0:
118 print 'Skipped %d invalid lines starting at line #%d: "%s"' % ( skipped_lines, first_invalid_line, invalid_line )