diff filtering.py @ 6:5742b322f956 draft default tip

Uploaded

--- a/filtering.py	Tue Jun 28 11:08:50 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,128 +0,0 @@
-#!/usr/bin/env python
-# This tool takes a tab-delimited text file as input and creates filters on columns based on certain properties.
-# The tool will skip over invalid lines within the file, informing the user about the number of lines skipped.
-
-from __future__ import division
-import sys, re, os.path
-from galaxy import eggs
-
-# Older py compatibility
-try:
-    set()
-except:
-    from sets import Set as set
-
-assert sys.version_info[:2] >= ( 2, 4 )
-
-def get_operands( filter_condition ):
-    # Note that the order of all_operators is important
-    items_to_strip = ['+', '-', '**', '*', '//', '/', '%', '<<', '>>', '&', '|', '^', '~', '<=', '<', '>=', '>', '==', '!=', '<>', ' and ', ' or ', ' not ', ' is ', ' is not ', ' in ', ' not in ']
-    for item in items_to_strip:
-        if filter_condition.find( item ) >= 0:
-            filter_condition = filter_condition.replace( item, ' ' )
-    operands = set( filter_condition.split( ' ' ) )
-    return operands
-
-def stop_err( msg ):
-    sys.stderr.write( msg )
-    sys.exit()
-
-in_fname = sys.argv[1]
-out_fname = sys.argv[2]
-cond_text = sys.argv[3]
-try:
-    in_columns = int( sys.argv[4] )
-    assert sys.argv[5]  #check to see that the column types varaible isn't null
-    in_column_types = sys.argv[5].split( ',' )
-except:
-    stop_err( "Data does not appear to be tabular.  This tool can only be used with tab-delimited data." )
-
-# Unescape if input has been escaped
-mapped_str = {
-    '__lt__': '<',
-    '__le__': '<=',
-    '__eq__': '==',
-    '__ne__': '!=',
-    '__gt__': '>',
-    '__ge__': '>=',
-    '__sq__': '\'',
-    '__dq__': '"',
-}
-for key, value in mapped_str.items():
-    cond_text = cond_text.replace( key, value )
-    
-# Attempt to determine if the condition includes executable stuff and, if so, exit
-secured = dir()
-operands = get_operands(cond_text)
-for operand in operands:
-    try:
-        check = int( operand )
-    except:
-        if operand in secured:
-            stop_err( "Illegal value '%s' in condition '%s'" % ( operand, cond_text ) )
-
-# Prepare the column variable names and wrappers for column data types
-cols, type_casts = [], []
-for col in range( 1, in_columns + 1 ):
-    col_name = "c%d" % col
-    cols.append( col_name )
-    col_type = in_column_types[ col - 1 ]
-    type_cast = "%s(%s)" % ( col_type, col_name )
-    type_casts.append( type_cast )
- 
-col_str = ', '.join( cols )    # 'c1, c2, c3, c4'
-type_cast_str = ', '.join( type_casts )  # 'str(c1), int(c2), int(c3), str(c4)'
-assign = "%s = line.split( '\\t' )" % col_str
-wrap = "%s = %s" % ( col_str, type_cast_str )
-skipped_lines = 0
-first_invalid_line = 0
-invalid_line = None
-lines_kept = 0
-total_lines = 0
-out = open( out_fname, 'wt' )
-    
-# Read and filter input file, skipping invalid lines
-code = '''
-for i, line in enumerate( file( in_fname ) ):
-    total_lines += 1
-    line = line.rstrip( '\\r\\n' )
-    if not line or line.startswith( '#' ):
-        skipped_lines += 1
-        if not invalid_line:
-            first_invalid_line = i + 1
-            invalid_line = line
-        continue
-    try:
-        %s
-        %s
-        if %s:
-            lines_kept += 1
-            print >> out, line
-    except:
-        skipped_lines += 1
-        if not invalid_line:
-            first_invalid_line = i + 1
-            invalid_line = line
-''' % ( assign, wrap, cond_text )
-
-valid_filter = True
-try:
-    exec code
-except Exception, e:
-    out.close()
-    if str( e ).startswith( 'invalid syntax' ):
-        valid_filter = False
-        stop_err( 'Filter condition "%s" likely invalid. See tool tips, syntax and examples.' % cond_text )
-    else:
-        stop_err( str( e ) )
-
-if valid_filter:
-    out.close()
-    valid_lines = total_lines - skipped_lines
-    print 'Filtering with %s, ' % cond_text
-    if valid_lines > 0:
-        print 'kept %4.2f%% of %d lines.' % ( 100.0*lines_kept/valid_lines, total_lines )
-    else:
-        print 'Possible invalid filter condition "%s" or non-existent column referenced. See tool tips, syntax and examples.' % cond_text
-    if skipped_lines > 0:
-        print 'Skipped %d invalid lines starting at line #%d: "%s"' % ( skipped_lines, first_invalid_line, invalid_line )