diff tools/filters/gff/gff_filter_by_attribute.py @ 0:9071e359b9a3

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/filters/gff/gff_filter_by_attribute.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,163 @@
+#!/usr/bin/env python
+# This tool takes a gff file as input and creates filters on attributes based on certain properties.
+# The tool will skip over invalid lines within the file, informing the user about the number of lines skipped.
+# TODO: much of this code is copied from the Filter1 tool (filtering.py in tools/stats/). The commonalities should be 
+# abstracted and leveraged in each filtering tool.
+
+from __future__ import division
+import sys
+from galaxy import eggs
+from galaxy.util.json import to_json_string, from_json_string
+
+# Older py compatibility
+try:
+    set()
+except:
+    from sets import Set as set
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+#
+# Helper functions.
+#
+
+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()
+
+def check_for_executable( text, description='' ):
+    # Attempt to determine if the condition includes executable stuff and, if so, exit.
+    secured = dir()
+    operands = get_operands( text )
+    for operand in operands:
+        try:
+            check = int( operand )
+        except:
+            if operand in secured:
+                stop_err( "Illegal value '%s' in %s '%s'" % ( operand, description, text ) )
+                
+#
+# Process inputs.
+#
+
+in_fname = sys.argv[1]
+out_fname = sys.argv[2]
+cond_text = sys.argv[3]
+attribute_types = from_json_string( sys.argv[4] )
+
+# Convert types from str to type objects.
+for name, a_type in attribute_types.items():
+    check_for_executable(a_type)
+    attribute_types[ name ] = eval( a_type )
+    
+# 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.
+check_for_executable( cond_text, 'condition')
+
+# Prepare the column variable names and wrappers for column data types. Only 
+# prepare columns up to largest column in condition.
+attrs, type_casts = [], []
+for name, attr_type in attribute_types.items():
+    attrs.append( name )
+    type_cast = "get_value('%(name)s', attribute_types['%(name)s'], attribute_values)" % ( {'name': name} )
+    type_casts.append( type_cast )
+    
+attr_str = ', '.join( attrs )    # 'c1, c2, c3, c4'
+type_cast_str = ', '.join( type_casts )  # 'str(c1), int(c2), int(c3), str(c4)'
+wrap = "%s = %s" % ( attr_str, type_cast_str )
+    
+# Stats 
+skipped_lines = 0
+first_invalid_line = 0
+invalid_line = None
+lines_kept = 0
+total_lines = 0
+out = open( out_fname, 'wt' )
+
+# Helper function to safely get and type cast a value in a dict.
+def get_value(name, a_type, values_dict):
+    if name in values_dict:
+        return (a_type)(values_dict[ name ])
+    else:
+        return None
+    
+# 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:
+        # Place attribute values into variables with attribute
+        # name; type casting is done as well.
+        elems = line.split( '\t' )
+        attribute_values = {}
+        for name_value_pair in elems[8].split(";"):
+            pair = name_value_pair.strip().split(" ")
+            if pair == '':
+                continue
+            name = pair[0].strip()
+            if name == '':
+                continue
+            # Need to strip double quote from value and typecast.
+            attribute_values[name] = pair[1].strip(" \\"")
+        %s
+        if %s:
+            lines_kept += 1
+            print >> out, line
+    except Exception, e:
+        print e
+        skipped_lines += 1
+        if not invalid_line:
+            first_invalid_line = i + 1
+            invalid_line = line
+''' % ( 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 )