mirror of
https://github.com/galaxyproject/galaxy.git
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277 lines
8.6 KiB
Python
277 lines
8.6 KiB
Python
#!/usr/bin/env python
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# This tool takes a tab-delimited text file as input and creates filters on columns based on certain properties.
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# The tool will skip over invalid lines within the file, informing the user about the number of lines skipped.
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from __future__ import division
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import sys, re, os.path
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from galaxy import eggs
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from ast import parse, Module, walk
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# Older py compatibility
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try:
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set()
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except:
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from sets import Set as set
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AST_NODE_TYPE_WHITELIST = [
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'Expr', 'Load',
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'Str', 'Num', 'BoolOp',
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'Compare', 'And', 'Eq',
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'NotEq', 'Or', 'GtE',
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'LtE', 'Lt', 'Gt',
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'BinOp', 'Add', 'Div',
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'Sub', 'Mult', 'Mod',
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'Pow', 'LShift', 'GShift',
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'BitAnd', 'BitOr', 'BitXor',
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'UnaryOp', 'Invert', 'Not',
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'NotIn', 'In', 'Is',
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'IsNot', 'List',
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'Index', 'Subscript',
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# Further checks
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'Name', 'Call', 'Attribute',
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]
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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'.split('|')
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STRING_AND_LIST_METHODS = [ name for name in dir('') + dir([]) if not name.startswith('_') ]
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VALID_FUNCTIONS = BUILTIN_AND_MATH_FUNCTIONS + STRING_AND_LIST_METHODS
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def __check_name( ast_node ):
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name = ast_node.id
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if re.match(r'^c\d+$', name):
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return True
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return name in VALID_FUNCTIONS
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def __check_attribute( ast_node ):
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attribute_name = ast_node.attr
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if attribute_name not in STRING_AND_LIST_METHODS:
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return False
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return True
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def __check_call( ast_node ):
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# If we are calling a function or method, it better be a math,
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# string or list function.
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ast_func = ast_node.func
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ast_func_class = ast_func.__class__.__name__
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if ast_func_class == 'Name':
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if ast_func.id not in BUILTIN_AND_MATH_FUNCTIONS:
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return False
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elif ast_func_class == 'Attribute':
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if not __check_attribute( ast_func ):
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return False
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else:
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return False
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return True
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def check_expression( text ):
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"""
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>>> check_expression("c1=='chr1' and c3-c2>=2000 and c6=='+'")
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True
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>>> check_expression("eval('1+1')")
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False
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>>> check_expression("import sys")
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False
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>>> check_expression("[].__str__")
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False
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>>> check_expression("__builtins__")
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False
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>>> check_expression("'x' in globals")
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False
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>>> check_expression("'x' in [1,2,3]")
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True
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>>> check_expression("c3=='chr1' and c5>5")
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True
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>>> check_expression("c3=='chr1' and d5>5") # Invalid d5 reference
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False
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>>> check_expression("c3=='chr1' and c5>5 or exec")
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False
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>>> check_expression("type(c1) != type(1)")
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True
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>>> check_expression("c1.split(',')[1] == '1'")
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True
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>>> check_expression("exec 1")
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False
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>>> check_expression("str(c2) in [\\\"a\\\",\\\"b\\\"]")
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True
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"""
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try:
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module = parse( text )
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except SyntaxError:
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return False
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if not isinstance(module, Module):
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return False
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statements = module.body
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if not len( statements ) == 1:
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return False
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expression = statements[0]
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if expression.__class__.__name__ != 'Expr':
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return False
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for ast_node in walk( expression ):
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ast_node_class = ast_node.__class__.__name__
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# Toss out everything that is not a "simple" expression,
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# imports, error handling, etc...
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if ast_node_class not in AST_NODE_TYPE_WHITELIST:
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return False
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# White-list more potentially dangerous types AST elements.
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if ast_node_class == 'Name':
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# In order to prevent loading 'exec', 'eval', etc...
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# put string restriction on names allowed.
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if not __check_name( ast_node ):
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return False
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# Check only valid, white-listed functions are called.
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elif ast_node_class == 'Call':
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if not __check_call( ast_node ):
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return False
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# Check only valid, white-listed attributes are accessed
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elif ast_node_class == 'Attribute':
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if not __check_attribute( ast_node ):
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return False
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return True
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def get_operands( filter_condition ):
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# Note that the order of all_operators is important
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items_to_strip = ['+', '-', '**', '*', '//', '/', '%', '<<', '>>', '&', '|', '^', '~', '<=', '<', '>=', '>', '==', '!=', '<>', ' and ', ' or ', ' not ', ' is ', ' is not ', ' in ', ' not in ']
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for item in items_to_strip:
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if filter_condition.find( item ) >= 0:
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filter_condition = filter_condition.replace( item, ' ' )
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operands = set( filter_condition.split( ' ' ) )
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return operands
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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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in_fname = sys.argv[1]
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out_fname = sys.argv[2]
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cond_text = sys.argv[3]
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try:
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in_columns = int( sys.argv[4] )
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assert sys.argv[5] #check to see that the column types variable isn't null
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in_column_types = sys.argv[5].split( ',' )
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except:
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stop_err( "Data does not appear to be tabular. This tool can only be used with tab-delimited data." )
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num_header_lines = int( sys.argv[6] )
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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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'__ob__': '[',
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'__cb__': ']',
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}
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for key, value in mapped_str.items():
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cond_text = cond_text.replace( key, value )
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# Attempt to determine if the condition includes executable stuff and, if so, exit
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secured = dir()
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operands = get_operands(cond_text)
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for operand in operands:
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try:
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check = int( operand )
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except:
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if operand in secured:
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stop_err( "Illegal value '%s' in condition '%s'" % ( operand, cond_text ) )
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if not check_expression(cond_text):
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stop_err( "Illegal/invalid in condition '%s'" % ( cond_text ) )
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# Work out which columns are used in the filter (save using 1 based counting)
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used_cols = sorted(set(int(match.group()[1:]) \
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for match in re.finditer('c(\d)+', cond_text)))
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largest_col_index = max(used_cols)
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# Prepare the column variable names and wrappers for column data types. Only
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# cast columns used in the filter.
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cols, type_casts = [], []
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for col in range( 1, largest_col_index + 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 ]
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if col in used_cols:
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type_cast = "%s(%s)" % ( col_type, col_name )
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else:
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#If we don't use this column, don't cast it.
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#Otherwise we get errors on things like optional integer columns.
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type_cast = 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' )[:%i]" % ( col_str, largest_col_index )
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wrap = "%s = %s" % ( col_str, type_cast_str )
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skipped_lines = 0
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invalid_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_fname, 'wt' )
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# Read and filter input file, skipping invalid lines
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code = '''
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for i, line in enumerate( file( in_fname ) ):
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total_lines += 1
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line = line.rstrip( '\\r\\n' )
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if i < num_header_lines:
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lines_kept += 1
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print >> out, line
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continue
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if not line or line.startswith( '#' ):
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skipped_lines += 1
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continue
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try:
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%s
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%s
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if %s:
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lines_kept += 1
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print >> out, line
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except:
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invalid_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, cond_text )
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valid_filter = 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_filter = False
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stop_err( 'Filter condition "%s" likely invalid. See tool tips, syntax and examples.' % cond_text )
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else:
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stop_err( str( e ) )
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if valid_filter:
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out.close()
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valid_lines = total_lines - skipped_lines
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print 'Filtering with %s, ' % cond_text
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if valid_lines > 0:
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print 'kept %4.2f%% of %d valid lines (%d total lines).' % ( 100.0*lines_kept/valid_lines, valid_lines, total_lines )
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else:
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print 'Possible invalid filter condition "%s" or non-existent column referenced. See tool tips, syntax and examples.' % cond_text
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if invalid_lines:
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print 'Skipped %d invalid line(s) starting at line #%d: "%s"' % ( invalid_lines, first_invalid_line, invalid_line )
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if skipped_lines:
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print 'Skipped %i comment (starting with #) or blank line(s)' % skipped_lines
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