<s> import sys , argparse <EOL> from smRtools import * <EOL> def masterListGenerator ( data_source ) : <EOL> for filePath , FileExt , FileLabel in data_source : <EOL> yield HandleSmRNAwindows ( filePath , FileExt , IndexSource , genomeRefFormat ) <EOL> def Parser ( ) : <EOL> the_parser = argparse . ArgumentParser ( ) <EOL> the_parser . add_argument ( '<STR_LIT>' , action = "<STR_LIT:store>" , type = str , help = "<STR_LIT>" ) <EOL> the_parser . add_argument ( '<STR_LIT>' , action = "<STR_LIT:store>" , type = str , choices = [ "<STR_LIT>" , "<STR_LIT>" ] , help = "<STR_LIT>" ) <EOL> the_parser . add_argument ( '<STR_LIT>' , action = "<STR_LIT:store>" , type = str , help = "<STR_LIT>" ) <EOL> the_parser . add_argument ( '<STR_LIT>' , choices = [ "<STR_LIT>" , "<STR_LIT>" , "<STR_LIT>" ] , help = "<STR_LIT>" ) <EOL> the_parser . add_argument ( '<STR_LIT>' , nargs = '<STR_LIT:+>' , help = "<STR_LIT>" ) <EOL> the_parser . add_argument ( '<STR_LIT>' , nargs = '<STR_LIT:+>' , help = "<STR_LIT>" ) <EOL> the_parser . add_argument ( '<STR_LIT>' , nargs = '<STR_LIT:+>' , help = "<STR_LIT>" ) <EOL> args = the_parser . parse_args ( ) <EOL> return args <EOL> args = Parser ( ) <EOL> IndexSource = args . IndexSource <EOL> genomeRefFormat = args . ExtractDirective <EOL> Output = args . output <EOL> Polarity = args . polarity <EOL> header = [ "<STR_LIT>" ] <EOL> FileLabelList = [ label for label in args . alignmentLabel ] <EOL> header . extend ( FileLabelList ) <EOL> assert ( len ( FileLabelList ) == len ( set ( FileLabelList ) ) ) , "<STR_LIT>" <EOL> data_source = zip ( args . alignmentSource , args . alignmentFormat , args . alignmentLabel ) <EOL> master_generator = masterListGenerator ( data_source ) <EOL> for i , window in enumerate ( master_generator ) : <EOL> window = window <EOL> if i == <NUM_LIT:0> : <EOL> gene_count_dict = { gene : [ str ( item . readcount ( polarity = Polarity ) ) ] for gene , item in window . instanceDict . items ( ) } <EOL> else : <EOL> [ gene_count_dict [ gene ] . append ( str ( item . readcount ( polarity = Polarity ) ) ) for gene , item in window . instanceDict . items ( ) ] <EOL> F = open ( args . output , "<STR_LIT:w>" ) <EOL> print >> F , "<STR_LIT:\t>" . join ( header ) <EOL> for item in sorted ( gene_count_dict . keys ( ) ) : <EOL> line = [ item ] <EOL> line . extend ( gene_count_dict [ item ] ) <EOL> print >> F , "<STR_LIT:\t>" . join ( line ) <EOL> F . close ( ) </s>
