<s> """<STR_LIT>""" <EOL> import os <EOL> import sys <EOL> import logging <EOL> from MACS2 . OptValidator import opt_validate_pileup as opt_validate <EOL> from MACS2 . OutputWriter import * <EOL> from MACS2 . Pileup import pileup_and_write <EOL> from MACS2 . Constants import * <EOL> def run ( o_options ) : <EOL> """<STR_LIT>""" <EOL> options = opt_validate ( o_options ) <EOL> info = options . info <EOL> warn = options . warn <EOL> debug = options . debug <EOL> error = options . error <EOL> assert options . format != '<STR_LIT>' , "<STR_LIT>" <EOL> outfile = os . path . join ( options . outdir , options . outputfile ) <EOL> if os . path . isfile ( outfile ) : <EOL> info ( "<STR_LIT>" % outfile ) <EOL> os . unlink ( outfile ) <EOL> info ( "<STR_LIT>" ) <EOL> ( tsize , treat ) = load_tag_files_options ( options ) <EOL> info ( "<STR_LIT>" , tsize ) <EOL> t0 = treat . total <EOL> info ( "<STR_LIT>" , t0 ) <EOL> if options . bothdirection : <EOL> info ( "<STR_LIT>" % options . extsize ) <EOL> pileup_and_write ( treat , outfile , options . extsize * <NUM_LIT:2> , <NUM_LIT:1> , directional = False , halfextension = False ) <EOL> else : <EOL> info ( "<STR_LIT>" % options . extsize ) <EOL> pileup_and_write ( treat , outfile , options . extsize , <NUM_LIT:1> , directional = True , halfextension = False ) <EOL> info ( "<STR_LIT>" % options . outputfile ) <EOL> def load_tag_files_options ( options ) : <EOL> """<STR_LIT>""" <EOL> options . info ( "<STR_LIT>" ) <EOL> tp = options . parser ( options . ifile [ <NUM_LIT:0> ] ) <EOL> tsize = tp . tsize ( ) <EOL> treat = tp . build_fwtrack ( ) <EOL> if len ( options . ifile ) > <NUM_LIT:1> : <EOL> for tfile in options . ifile [ <NUM_LIT:1> : ] : <EOL> tp = options . parser ( tfile ) <EOL> treat = tp . append_fwtrack ( treat ) <EOL> treat . finalize ( ) <EOL> options . info ( "<STR_LIT>" % tsize ) <EOL> return ( tsize , treat ) </s>
