<s> """<STR_LIT>""" <EOL> import os <EOL> import sys <EOL> import re <EOL> from subprocess import Popen , PIPE <EOL> from optparse import OptionParser <EOL> def check_Rscript_BEDTools ( ) : <EOL> try : <EOL> p = Popen ( [ "<STR_LIT>" , "<STR_LIT>" , "<STR_LIT>" ] , stdout = PIPE , stderr = PIPE ) <EOL> except OSError as ( errno , detail ) : <EOL> sys . stderr . write ( "<STR_LIT>" ) <EOL> sys . stderr . write ( "<STR_LIT>" % ( errno , detail ) ) <EOL> sys . stderr . write ( "<STR_LIT>" ) <EOL> sys . exit ( <NUM_LIT:1> ) <EOL> try : <EOL> p = Popen ( [ "<STR_LIT>" , "<STR_LIT>" ] , stdout = PIPE , stderr = PIPE ) <EOL> except OSError as ( errno , detail ) : <EOL> sys . stderr . write ( "<STR_LIT>" ) <EOL> sys . stderr . write ( "<STR_LIT>" % ( errno , detail ) ) <EOL> sys . stderr . write ( "<STR_LIT>" ) <EOL> sys . exit ( <NUM_LIT:1> ) <EOL> def main ( ) : <EOL> check_Rscript_BEDTools ( ) <EOL> usage = "<STR_LIT>" <EOL> description = "<STR_LIT>" <EOL> optparser = OptionParser ( version = "<STR_LIT>" , description = description , usage = usage , add_help_option = False ) <EOL> optparser . add_option ( "<STR_LIT>" , "<STR_LIT>" , action = "<STR_LIT>" , help = "<STR_LIT>" ) <EOL> optparser . add_option ( "<STR_LIT>" , "<STR_LIT>" , dest = "<STR_LIT>" , type = "<STR_LIT:string>" , <EOL> help = "<STR_LIT>" ) <EOL> optparser . add_option ( "<STR_LIT>" , "<STR_LIT>" , dest = "<STR_LIT>" , type = "<STR_LIT:string>" , <EOL> help = "<STR_LIT>" ) <EOL> optparser . add_option ( "<STR_LIT>" , "<STR_LIT>" , dest = "<STR_LIT>" , type = "<STR_LIT:float>" , <EOL> help = "<STR_LIT>" , default = <NUM_LIT> ) <EOL> ( options , args ) = optparser . parse_args ( ) <EOL> if not options . ifile or not options . jfile : <EOL> print "<STR_LIT>" <EOL> sys . exit ( <NUM_LIT:1> ) <EOL> gsize = int ( options . gsize ) <EOL> p = Popen ( [ "<STR_LIT>" , "<STR_LIT>" , options . ifile , "<STR_LIT>" , options . jfile , "<STR_LIT>" ] , stdout = PIPE ) <EOL> q = Popen ( [ "<STR_LIT>" , "<STR_LIT>" , options . ifile , "<STR_LIT>" , options . jfile , "<STR_LIT>" ] , stdout = PIPE ) <EOL> coverage2 = [ <NUM_LIT:0> , <NUM_LIT:0> ] <EOL> for i in p . stdout : <EOL> if i . startswith ( '<STR_LIT:all>' ) : <EOL> ( tmp , depth , cover , len2 , percentage ) = i . strip ( ) . split ( ) <EOL> if int ( depth ) > <NUM_LIT:0> : <EOL> coverage2 [ <NUM_LIT:1> ] += int ( cover ) <EOL> coverage2 [ <NUM_LIT:0> ] = int ( len2 ) <EOL> coverage1 = [ <NUM_LIT:0> , <NUM_LIT:0> ] <EOL> for i in q . stdout : <EOL> if i . startswith ( '<STR_LIT:all>' ) : <EOL> ( tmp , depth , cover , len1 , percentage ) = i . strip ( ) . split ( ) <EOL> if int ( depth ) > <NUM_LIT:0> : <EOL> coverage1 [ <NUM_LIT:1> ] += int ( cover ) <EOL> coverage1 [ <NUM_LIT:0> ] = int ( len1 ) <EOL> if coverage1 [ <NUM_LIT:1> ] != coverage2 [ <NUM_LIT:1> ] : <EOL> print "<STR_LIT>" <EOL> print coverage1 <EOL> print coverage2 <EOL> print "<STR_LIT>" <EOL> sys . exit ( <NUM_LIT:1> ) <EOL> common = float ( coverage1 [ <NUM_LIT:1> ] ) <EOL> only1 = float ( coverage1 [ <NUM_LIT:0> ] - coverage1 [ <NUM_LIT:1> ] ) <EOL> only2 = float ( coverage2 [ <NUM_LIT:0> ] - coverage2 [ <NUM_LIT:1> ] ) <EOL> r = "<STR_LIT>" % ( common , common + only1 , gsize - common - only1 , common + only2 ) <EOL> p = Popen ( [ "<STR_LIT>" , "<STR_LIT>" , r ] , stdout = PIPE , stderr = PIPE ) <EOL> for i in p . stdout : <EOL> if i . startswith ( "<STR_LIT>" ) : <EOL> i = i . strip ( ) <EOL> print "<STR_LIT>" % ( abs ( - <NUM_LIT:1> * float ( i [ i . find ( "<STR_LIT>" ) + <NUM_LIT:3> : ] ) ) ) <EOL> p . terminate ( ) <EOL> r = "<STR_LIT>" % ( common , common + only1 , gsize - common - only1 , common + only2 ) <EOL> p = Popen ( [ "<STR_LIT>" , "<STR_LIT>" , r ] , stdout = PIPE , stderr = PIPE ) <EOL> for i in p . stdout : <EOL> if i . startswith ( "<STR_LIT>" ) : <EOL> i = i . strip ( ) <EOL> print "<STR_LIT>" % ( abs ( - <NUM_LIT:1> * float ( i [ i . find ( "<STR_LIT>" ) + <NUM_LIT:3> : ] ) ) ) <EOL> p . terminate ( ) <EOL> if __name__ == '<STR_LIT:__main__>' : <EOL> try : <EOL> main ( ) <EOL> except KeyboardInterrupt : <EOL> sys . stderr . write ( "<STR_LIT>" ) <EOL> sys . exit ( <NUM_LIT:0> ) </s>
