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126 lines
4.9 KiB
Python
126 lines
4.9 KiB
Python
#!/usr/bin/env python
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# This tool takes a tab-delimited textfile as input and creates another column in the file which is the result of
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# a computation performed on every row in the original file. The tool will skip over invalid lines within the file,
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# informing the user about the number of lines skipped.
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import sys, re
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# These functions may be used in compute expression:
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from math import log,exp,sqrt,ceil,floor
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assert sys.version_info[:2] >= ( 2, 4 )
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def stop_err( msg ):
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sys.stderr.write( msg )
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sys.exit()
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inp_file = sys.argv[1]
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out_file = sys.argv[2]
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expr = sys.argv[3]
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round_result = sys.argv[4]
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try:
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in_columns = int( sys.argv[5] )
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except:
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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." )
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if in_columns < 2:
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# To be considered tabular, data must fulfill requirements of the sniff.is_column_based() method.
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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." )
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try:
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in_column_types = sys.argv[6].split( ',' )
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except:
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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." )
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if len( in_column_types ) != in_columns:
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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." )
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# Unescape if input has been escaped
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mapped_str = {
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'__lt__': '<',
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'__le__': '<=',
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'__eq__': '==',
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'__ne__': '!=',
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'__gt__': '>',
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'__ge__': '>=',
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'__sq__': '\'',
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'__dq__': '"',
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}
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for key, value in mapped_str.items():
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expr = expr.replace( key, value )
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operators = 'is|not|or|and'
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builtin_and_math_functions = 'abs|all|any|bin|chr|cmp|complex|divmod|float|hex|int|len|long|max|min|oct|ord|pow|range|reversed|round|sorted|str|sum|type|unichr|unicode|log|exp|sqrt|ceil|floor'
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string_and_list_methods = [ name for name in dir('') + dir([]) if not name.startswith('_') ]
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whitelist = "^([c0-9\+\-\*\/\(\)\.\'\"><=,:! ]|%s|%s|%s)*$" % (operators, builtin_and_math_functions, '|'.join(string_and_list_methods))
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if not re.compile(whitelist).match(expr):
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stop_err("Invalid expression")
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# Prepare the column variable names and wrappers for column data types
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cols, type_casts = [], []
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for col in range( 1, in_columns + 1 ):
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col_name = "c%d" % col
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cols.append( col_name )
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col_type = in_column_types[ col - 1 ].strip()
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if round_result == 'no' and col_type == 'int':
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col_type = 'float'
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type_cast = "%s(%s)" % ( col_type, col_name )
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type_casts.append( type_cast )
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col_str = ', '.join( cols ) # 'c1, c2, c3, c4'
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type_cast_str = ', '.join( type_casts ) # 'str(c1), int(c2), int(c3), str(c4)'
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assign = "%s = line.split( '\\t' )" % col_str
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wrap = "%s = %s" % ( col_str, type_cast_str )
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skipped_lines = 0
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first_invalid_line = 0
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invalid_line = None
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lines_kept = 0
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total_lines = 0
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out = open( out_file, 'wt' )
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# Read input file, skipping invalid lines, and perform computation that will result in a new column
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code = '''
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for i, line in enumerate( file( inp_file ) ):
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total_lines += 1
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line = line.rstrip( '\\r\\n' )
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if not line or line.startswith( '#' ):
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skipped_lines += 1
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if not invalid_line:
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first_invalid_line = i + 1
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invalid_line = line
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continue
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try:
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%s
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%s
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new_val = %s
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if round_result == "yes":
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new_val = int( round( new_val ) )
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new_line = line + '\\t' + str( new_val )
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print >> out, new_line
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lines_kept += 1
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except:
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skipped_lines += 1
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if not invalid_line:
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first_invalid_line = i + 1
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invalid_line = line
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''' % ( assign, wrap, expr )
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valid_expr = True
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try:
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exec code
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except Exception, e:
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out.close()
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if str( e ).startswith( 'invalid syntax' ):
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valid_expr = False
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stop_err( 'Expression "%s" likely invalid. See tool tips, syntax and examples.' % expr )
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else:
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stop_err( str( e ) )
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if valid_expr:
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out.close()
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valid_lines = total_lines - skipped_lines
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print 'Creating column %d with expression %s' % ( in_columns + 1, expr )
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if valid_lines > 0:
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print 'kept %4.2f%% of %d lines.' % ( 100.0*lines_kept/valid_lines, total_lines )
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else:
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print 'Possible invalid expression "%s" or non-existent column referenced. See tool tips, syntax and examples.' % expr
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if skipped_lines > 0:
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print 'Skipped %d invalid lines starting at line #%d: "%s"' % ( skipped_lines, first_invalid_line, invalid_line )
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