Mercurial > repos > devteam > column_maker
annotate column_maker.py @ 3:35937a6b04fb draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit f6e96ffa420035051ea4632596dfd171074aa66d
| author | devteam |
|---|---|
| date | Thu, 25 Oct 2018 17:31:05 -0400 |
| parents | 292c605c2dc7 |
| children | 3335c0d583d8 |
| rev | line source |
|---|---|
| 0 | 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 | |
| 6 import sys, re | |
| 7 # These functions may be used in compute expression: | |
| 8 from math import log,exp,sqrt,ceil,floor | |
| 9 | |
| 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 operators = 'is|not|or|and' | |
|
2
292c605c2dc7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents:
0
diff
changeset
|
50 builtin_and_math_functions = 'abs|all|any|bin|chr|cmp|complex|divmod|float|bool|hex|int|len|long|max|min|oct|ord|pow|range|reversed|round|sorted|str|sum|type|unichr|unicode|log|exp|sqrt|ceil|floor' |
| 0 | 51 string_and_list_methods = [ name for name in dir('') + dir([]) if not name.startswith('_') ] |
| 52 whitelist = "^([c0-9\+\-\*\/\(\)\.\'\"><=,:! ]|%s|%s|%s)*$" % (operators, builtin_and_math_functions, '|'.join(string_and_list_methods)) | |
| 53 if not re.compile(whitelist).match(expr): | |
| 54 stop_err("Invalid expression") | |
| 55 | |
| 56 # Prepare the column variable names and wrappers for column data types | |
| 57 cols, type_casts = [], [] | |
| 58 for col in range( 1, in_columns + 1 ): | |
| 59 col_name = "c%d" % col | |
| 60 cols.append( col_name ) | |
| 61 col_type = in_column_types[ col - 1 ].strip() | |
| 62 if round_result == 'no' and col_type == 'int': | |
| 63 col_type = 'float' | |
| 64 type_cast = "%s(%s)" % ( col_type, col_name ) | |
| 65 type_casts.append( type_cast ) | |
| 66 | |
| 67 col_str = ', '.join( cols ) # 'c1, c2, c3, c4' | |
| 68 type_cast_str = ', '.join( type_casts ) # 'str(c1), int(c2), int(c3), str(c4)' | |
| 69 assign = "%s = line.split( '\\t' )" % col_str | |
| 70 wrap = "%s = %s" % ( col_str, type_cast_str ) | |
| 71 skipped_lines = 0 | |
| 72 first_invalid_line = 0 | |
| 73 invalid_line = None | |
| 74 lines_kept = 0 | |
| 75 total_lines = 0 | |
| 76 out = open( out_file, 'wt' ) | |
| 77 | |
| 78 # Read input file, skipping invalid lines, and perform computation that will result in a new column | |
| 79 code = ''' | |
| 80 for i, line in enumerate( file( inp_file ) ): | |
| 81 total_lines += 1 | |
| 82 line = line.rstrip( '\\r\\n' ) | |
| 83 if not line or line.startswith( '#' ): | |
| 84 skipped_lines += 1 | |
| 85 if not invalid_line: | |
| 86 first_invalid_line = i + 1 | |
| 87 invalid_line = line | |
| 88 continue | |
| 89 try: | |
| 90 %s | |
| 91 %s | |
| 92 new_val = %s | |
| 93 if round_result == "yes": | |
| 94 new_val = int( round( new_val ) ) | |
| 95 new_line = line + '\\t' + str( new_val ) | |
| 96 print >> out, new_line | |
| 97 lines_kept += 1 | |
| 98 except: | |
| 99 skipped_lines += 1 | |
| 100 if not invalid_line: | |
| 101 first_invalid_line = i + 1 | |
| 102 invalid_line = line | |
| 103 ''' % ( assign, wrap, expr ) | |
| 104 | |
| 105 valid_expr = True | |
| 106 try: | |
| 107 exec code | |
| 108 except Exception, e: | |
| 109 out.close() | |
| 110 if str( e ).startswith( 'invalid syntax' ): | |
| 111 valid_expr = False | |
| 112 stop_err( 'Expression "%s" likely invalid. See tool tips, syntax and examples.' % expr ) | |
| 113 else: | |
| 114 stop_err( str( e ) ) | |
| 115 | |
| 116 if valid_expr: | |
| 117 out.close() | |
| 118 valid_lines = total_lines - skipped_lines | |
| 119 print 'Creating column %d with expression %s' % ( in_columns + 1, expr ) | |
| 120 if valid_lines > 0: | |
| 121 print 'kept %4.2f%% of %d lines.' % ( 100.0*lines_kept/valid_lines, total_lines ) | |
| 122 else: | |
| 123 print 'Possible invalid expression "%s" or non-existent column referenced. See tool tips, syntax and examples.' % expr | |
| 124 if skipped_lines > 0: | |
| 125 print 'Skipped %d invalid lines starting at line #%d: "%s"' % ( skipped_lines, first_invalid_line, invalid_line ) |