<s> import numpy as np <EOL> import fastStructure <EOL> import parse_bed <EOL> import parse_str <EOL> import random <EOL> import getopt <EOL> import sys <EOL> import pdb <EOL> import warnings <EOL> warnings . filterwarnings ( '<STR_LIT:ignore>' , '<STR_LIT>' , ) <EOL> warnings . filterwarnings ( '<STR_LIT:ignore>' , '<STR_LIT>' , ) <EOL> def parseopts ( opts ) : <EOL> """<STR_LIT>""" <EOL> params = { '<STR_LIT>' : <NUM_LIT> , <EOL> '<STR_LIT>' : "<STR_LIT>" , <EOL> '<STR_LIT>' : <NUM_LIT:0> , <EOL> '<STR_LIT>' : False , <EOL> '<STR_LIT>' : '<STR_LIT>' <EOL> } <EOL> for opt , arg in opts : <EOL> if opt in [ "<STR_LIT>" ] : <EOL> params [ '<STR_LIT>' ] = int ( arg ) <EOL> elif opt in [ "<STR_LIT>" ] : <EOL> params [ '<STR_LIT>' ] = arg <EOL> elif opt in [ "<STR_LIT>" ] : <EOL> params [ '<STR_LIT>' ] = arg <EOL> elif opt in [ "<STR_LIT>" ] : <EOL> params [ '<STR_LIT>' ] = arg <EOL> if params [ '<STR_LIT>' ] not in [ '<STR_LIT>' , '<STR_LIT>' ] : <EOL> print "<STR_LIT>" <EOL> params [ '<STR_LIT>' ] = '<STR_LIT>' <EOL> elif opt in [ "<STR_LIT>" ] : <EOL> params [ '<STR_LIT>' ] = arg <EOL> elif opt in [ "<STR_LIT>" ] : <EOL> params [ '<STR_LIT>' ] = int ( arg ) <EOL> elif opt in [ "<STR_LIT>" ] : <EOL> params [ '<STR_LIT>' ] = float ( arg ) <EOL> elif opt in [ "<STR_LIT>" ] : <EOL> params [ '<STR_LIT>' ] = True <EOL> elif opt in [ "<STR_LIT>" ] : <EOL> np . random . seed ( int ( arg ) ) <EOL> random . seed ( int ( arg ) ) <EOL> return params <EOL> def checkopts ( params ) : <EOL> """<STR_LIT>""" <EOL> if params [ '<STR_LIT>' ] <= <NUM_LIT:0> : <EOL> print "<STR_LIT>" <EOL> raise ValueError <EOL> if params [ '<STR_LIT>' ] < <NUM_LIT:0> : <EOL> print "<STR_LIT>" <EOL> raise ValueError <EOL> if not params . has_key ( '<STR_LIT>' ) : <EOL> print "<STR_LIT>" <EOL> raise KeyError <EOL> if params [ '<STR_LIT>' ] not in [ '<STR_LIT>' , '<STR_LIT:str>' ] : <EOL> print "<STR_LIT>" <EOL> raise ValueError <EOL> if params [ '<STR_LIT>' ] <= <NUM_LIT:0> : <EOL> print "<STR_LIT>" <EOL> raise ValueError <EOL> if not params . has_key ( '<STR_LIT>' ) : <EOL> print "<STR_LIT>" <EOL> raise KeyError <EOL> if not params . has_key ( '<STR_LIT>' ) : <EOL> print "<STR_LIT>" <EOL> raise KeyError <EOL> def write_output ( Q , P , other , params ) : <EOL> """<STR_LIT>""" <EOL> handle = open ( '<STR_LIT>' % ( params [ '<STR_LIT>' ] , params [ '<STR_LIT>' ] ) , '<STR_LIT:w>' ) <EOL> handle . write ( '<STR_LIT:\n>' . join ( [ '<STR_LIT:U+0020>' . join ( [ '<STR_LIT>' % i for i in q ] ) for q in Q ] ) + '<STR_LIT:\n>' ) <EOL> handle . close ( ) <EOL> handle = open ( '<STR_LIT>' % ( params [ '<STR_LIT>' ] , params [ '<STR_LIT>' ] ) , '<STR_LIT:w>' ) <EOL> handle . write ( '<STR_LIT:\n>' . join ( [ '<STR_LIT:U+0020>' . join ( [ '<STR_LIT>' % i for i in p ] ) for p in P ] ) + '<STR_LIT:\n>' ) <EOL> handle . close ( ) <EOL> if params [ '<STR_LIT>' ] : <EOL> handle = open ( '<STR_LIT>' % ( params [ '<STR_LIT>' ] , params [ '<STR_LIT>' ] ) , '<STR_LIT:w>' ) <EOL> handle . write ( '<STR_LIT:\n>' . join ( [ '<STR_LIT:U+0020>' . join ( [ '<STR_LIT>' % i for i in q ] ) for q in other [ '<STR_LIT>' ] ] ) + '<STR_LIT:\n>' ) <EOL> handle . close ( ) <EOL> handle = open ( '<STR_LIT>' % ( params [ '<STR_LIT>' ] , params [ '<STR_LIT>' ] ) , '<STR_LIT:w>' ) <EOL> handle . write ( '<STR_LIT:\n>' . join ( [ '<STR_LIT:U+0020>' . join ( [ '<STR_LIT>' % i for i in np . hstack ( ( pb , pg ) ) ] ) for pb , pg in zip ( other [ '<STR_LIT>' ] , other [ '<STR_LIT>' ] ) ] ) + '<STR_LIT:\n>' ) <EOL> handle . close ( ) <EOL> def usage ( ) : <EOL> """<STR_LIT>""" <EOL> print "<STR_LIT>" <EOL> print "<STR_LIT>" % sys . argv [ <NUM_LIT:0> ] <EOL> print "<STR_LIT>" <EOL> print "<STR_LIT>" <EOL> print "<STR_LIT>" <EOL> print "<STR_LIT>" <EOL> print "<STR_LIT>" <EOL> print "<STR_LIT>" <EOL> print "<STR_LIT>" <EOL> print "<STR_LIT>" <EOL> print "<STR_LIT>" <EOL> if __name__ == "<STR_LIT:__main__>" : <EOL> argv = sys . argv [ <NUM_LIT:1> : ] <EOL> smallflags = "<STR_LIT>" <EOL> bigflags = [ "<STR_LIT>" , "<STR_LIT>" , "<STR_LIT>" , "<STR_LIT>" , "<STR_LIT>" , "<STR_LIT>" , "<STR_LIT>" , "<STR_LIT>" ] <EOL> try : <EOL> opts , args = getopt . getopt ( argv , smallflags , bigflags ) <EOL> if not opts : <EOL> usage ( ) <EOL> sys . exit ( <NUM_LIT:2> ) <EOL> except getopt . GetoptError : <EOL> print "<STR_LIT>" <EOL> usage ( ) <EOL> sys . exit ( <NUM_LIT:2> ) <EOL> params = parseopts ( opts ) <EOL> try : <EOL> checkopts ( params ) <EOL> except ( ValueError , KeyError ) : <EOL> sys . exit ( <NUM_LIT:2> ) <EOL> if params [ '<STR_LIT>' ] == '<STR_LIT>' : <EOL> G = parse_bed . load ( params [ '<STR_LIT>' ] ) <EOL> elif params [ '<STR_LIT>' ] == '<STR_LIT:str>' : <EOL> G = parse_str . load ( params [ '<STR_LIT>' ] ) <EOL> G = np . require ( G , dtype = np . uint8 , requirements = '<STR_LIT:C>' ) <EOL> Q , P , other = fastStructure . infer_variational_parameters ( G , params [ '<STR_LIT>' ] , params [ '<STR_LIT>' ] , params [ '<STR_LIT>' ] , params [ '<STR_LIT>' ] , params [ '<STR_LIT>' ] ) <EOL> write_output ( Q , P , other , params ) </s>
