<s> '''<STR_LIT>''' <EOL> import sys <EOL> import os <EOL> import glob <EOL> import imp <EOL> import collections <EOL> import pandas <EOL> import CGAT . Experiment as E <EOL> import CGAT . IOTools as IOTools <EOL> ORIGINAL_START = None <EOL> PARSER = None <EOL> EXPRESSIONS = ( <EOL> ( '<STR_LIT>' , '<STR_LIT>' ) , ) <EOL> EXCLUDE = ( "<STR_LIT>" , <EOL> "<STR_LIT>" , ) <EOL> class DummyError ( Exception ) : <EOL> pass <EOL> def LocalStart ( parser , * args , ** kwargs ) : <EOL> '''<STR_LIT>''' <EOL> global PARSER <EOL> PARSER = ORIGINAL_START ( parser , <EOL> return_parser = True , <EOL> ** kwargs <EOL> ) <EOL> raise DummyError ( ) <EOL> def collectOptionsFromScript ( script_name ) : <EOL> '''<STR_LIT>''' <EOL> prefix , suffix = os . path . splitext ( script_name ) <EOL> dirname = os . path . dirname ( script_name ) <EOL> basename = os . path . basename ( script_name ) [ : - <NUM_LIT:3> ] <EOL> if os . path . exists ( prefix + "<STR_LIT>" ) : <EOL> os . remove ( prefix + "<STR_LIT>" ) <EOL> with IOTools . openFile ( script_name ) as inf : <EOL> if "<STR_LIT>" in inf . read ( ) : <EOL> E . warn ( "<STR_LIT>" % script_name ) <EOL> return [ ] <EOL> try : <EOL> module = imp . load_source ( basename , script_name ) <EOL> except ImportError , msg : <EOL> E . warn ( '<STR_LIT>' % ( basename , msg ) ) <EOL> return [ ] <EOL> E . Start = LocalStart <EOL> try : <EOL> module . main ( argv = [ "<STR_LIT>" ] ) <EOL> except AttributeError : <EOL> E . warn ( "<STR_LIT>" % script_name ) <EOL> return [ ] <EOL> except SystemExit : <EOL> E . warn ( "<STR_LIT>" ) <EOL> return [ ] <EOL> except DummyError : <EOL> pass <EOL> result = [ ] <EOL> for option in PARSER . option_list : <EOL> if option . dest is None : <EOL> continue <EOL> optstring = option . get_opt_string ( ) <EOL> if optstring . startswith ( "<STR_LIT>" ) : <EOL> optstring = optstring [ <NUM_LIT:2> : ] <EOL> result . append ( optstring ) <EOL> return result <EOL> def main ( argv = None ) : <EOL> """<STR_LIT>""" <EOL> if argv is None : <EOL> argv = sys . argv <EOL> parser = E . OptionParser ( version = "<STR_LIT>" , <EOL> usage = globals ( ) [ "<STR_LIT>" ] ) <EOL> parser . add_option ( <EOL> "<STR_LIT>" , dest = "<STR_LIT>" , action = "<STR_LIT:store_true>" , <EOL> help = "<STR_LIT>" <EOL> "<STR_LIT>" <EOL> "<STR_LIT>" ) <EOL> parser . add_option ( <EOL> "<STR_LIT>" , dest = "<STR_LIT>" , type = "<STR_LIT:string>" , <EOL> help = "<STR_LIT>" <EOL> "<STR_LIT>" ) <EOL> parser . set_defaults ( <EOL> inplace = False , <EOL> tsv_file = None ) <EOL> ( options , args ) = E . Start ( parser , argv = argv ) <EOL> old_options = None <EOL> if options . tsv_file : <EOL> if not os . path . exists ( options . tsv_file ) : <EOL> raise OSError ( <EOL> "<STR_LIT>" % <EOL> options . tsv_file ) <EOL> old_options = pandas . read_csv ( <EOL> IOTools . openFile ( options . tsv_file ) , <EOL> sep = "<STR_LIT:\t>" , <EOL> index_col = <NUM_LIT:0> , <EOL> ) <EOL> old_options = old_options . fillna ( "<STR_LIT>" ) <EOL> global ORIGINAL_START <EOL> ORIGINAL_START = E . Start <EOL> all_options = collections . defaultdict ( list ) <EOL> for label , expression in EXPRESSIONS : <EOL> files = glob . glob ( expression ) <EOL> files . sort ( ) <EOL> for f in files : <EOL> E . debug ( "<STR_LIT>" % f ) <EOL> if os . path . isdir ( f ) : <EOL> continue <EOL> if os . path . basename ( f ) in EXCLUDE : <EOL> continue <EOL> collected_options = collectOptionsFromScript ( os . path . abspath ( f ) ) <EOL> for o in collected_options : <EOL> all_options [ o ] . append ( f ) <EOL> for x in old_options . index : <EOL> if x not in all_options : <EOL> all_options [ x ] . append ( "<STR_LIT>" ) <EOL> if options . inplace : <EOL> outfile = IOTools . openFile ( options . tsv_file , "<STR_LIT:w>" ) <EOL> E . info ( "<STR_LIT>" % options . tsv_file ) <EOL> else : <EOL> outfile = options . stdout <EOL> outfile . write ( "<STR_LIT>" ) <EOL> for o , v in sorted ( all_options . items ( ) ) : <EOL> try : <EOL> action , comment , alternative , ff = old_options . xs ( o ) <EOL> except KeyError : <EOL> action , comment , alternative , ff = "<STR_LIT>" , "<STR_LIT>" , "<STR_LIT>" , "<STR_LIT>" <EOL> if comment == "<STR_LIT>" : <EOL> comment = "<STR_LIT>" <EOL> if alternative == "<STR_LIT>" : <EOL> alternative = "<STR_LIT>" <EOL> outfile . write ( "<STR_LIT:\t>" . join ( ( map ( <EOL> str , ( o , action , comment , alternative , "<STR_LIT:U+002C>" . join ( v ) ) ) ) ) + "<STR_LIT:\n>" ) <EOL> if outfile != options . stdout : <EOL> outfile . close ( ) <EOL> E . Stop ( ) <EOL> if __name__ == "<STR_LIT:__main__>" : <EOL> sys . exit ( main ( sys . argv ) ) </s>
