<s> """<STR_LIT>""" <EOL> import sys <EOL> import os <EOL> import logging <EOL> from MACS2 . IO import BedGraphIO <EOL> from MACS2 . OptValidator import opt_validate_bdgopt as opt_validate <EOL> logging . basicConfig ( level = <NUM_LIT:20> , <EOL> format = '<STR_LIT>' , <EOL> datefmt = '<STR_LIT>' , <EOL> stream = sys . stderr , <EOL> filemode = "<STR_LIT:w>" <EOL> ) <EOL> error = logging . critical <EOL> warn = logging . warning <EOL> debug = logging . debug <EOL> info = logging . info <EOL> def run ( options ) : <EOL> options = opt_validate ( options ) <EOL> info ( "<STR_LIT>" ) <EOL> bio = BedGraphIO . bedGraphIO ( options . ifile ) <EOL> btrack = bio . build_bdgtrack ( baseline_value = <NUM_LIT:0> ) <EOL> info ( "<STR_LIT>" ) <EOL> if options . method . lower ( ) == "<STR_LIT>" : <EOL> btrack . p2q ( ) <EOL> elif options . method . lower ( ) == "<STR_LIT>" : <EOL> btrack . analen ( ) <EOL> else : <EOL> extraparam = float ( options . extraparam [ <NUM_LIT:0> ] ) <EOL> if options . method . lower ( ) == "<STR_LIT>" : <EOL> btrack . apply_func ( lambda x : x * extraparam ) <EOL> elif options . method . lower ( ) == "<STR_LIT>" : <EOL> btrack . apply_func ( lambda x : x + extraparam ) <EOL> elif options . method . lower ( ) == "<STR_LIT>" : <EOL> btrack . apply_func ( lambda x : x if x > extraparam else extraparam ) <EOL> elif options . method . lower ( ) == "<STR_LIT>" : <EOL> btrack . apply_func ( lambda x : x if x < extraparam else extraparam ) <EOL> ofile = os . path . join ( options . outdir , options . ofile ) <EOL> info ( "<STR_LIT>" ) <EOL> ofhd = open ( ofile , "<STR_LIT:wb>" ) <EOL> btrack . write_bedGraph ( ofhd , name = "<STR_LIT>" % ( options . method . upper ( ) ) , description = "<STR_LIT>" % ( options . method . upper ( ) ) ) <EOL> info ( "<STR_LIT>" % ( options . method , ofile ) ) </s>
