<s> '''<STR_LIT>''' <EOL> import os <EOL> import sys <EOL> import re <EOL> import optparse <EOL> import subprocess <EOL> import signal <EOL> import glob <EOL> import argparse <EOL> import multiprocessing . pool <EOL> import CGAT . Experiment as E <EOL> import CGAT . IOTools as IOTools <EOL> DISABLE = False <EOL> def subprocess_setup ( ) : <EOL> signal . signal ( signal . SIGPIPE , signal . SIG_DFL ) <EOL> def die ( msg = None ) : <EOL> if msg is not None : <EOL> print >> sys . stderr , msg <EOL> sys . exit ( <NUM_LIT:1> ) <EOL> def runCommand ( args ) : <EOL> cmd , logfile = args <EOL> log = open ( logfile , "<STR_LIT:w>" ) <EOL> log . write ( "<STR_LIT>" % "<STR_LIT:U+0020>" . join ( cmd ) ) <EOL> retcode = subprocess . call ( cmd , <EOL> preexec_fn = subprocess_setup , <EOL> stderr = log ) <EOL> if retcode != <NUM_LIT:0> : <EOL> die ( "<STR_LIT>" + str ( retcode ) ) <EOL> log . close ( ) <EOL> def main ( argv = None ) : <EOL> """<STR_LIT>""" <EOL> if DISABLE : <EOL> print "<STR_LIT>" <EOL> argv [ <NUM_LIT:0> ] = "<STR_LIT>" <EOL> runCommand ( argv , "<STR_LIT>" ) <EOL> return <NUM_LIT:0> <EOL> E . Start ( no_parsing = True ) <EOL> parser = argparse . ArgumentParser ( description = '<STR_LIT>' ) <EOL> parser . add_argument ( '<STR_LIT>' , '<STR_LIT>' , metavar = '<STR_LIT:N>' , type = int , dest = '<STR_LIT>' , <EOL> help = '<STR_LIT>' ) <EOL> parser . add_argument ( '<STR_LIT>' , action = '<STR_LIT:version>' , version = '<STR_LIT>' ) <EOL> options , args = parser . parse_known_args ( argv [ <NUM_LIT:1> : ] ) <EOL> E . info ( "<STR_LIT>" % options . nthreads ) <EOL> x = argv . index ( "<STR_LIT>" ) + <NUM_LIT:1> <EOL> all_options = argv [ <NUM_LIT:1> : x ] <EOL> ( input_missing_reads , input_genome , <EOL> output_junctions , <EOL> output_insertions , output_deletions , <EOL> input_left_all_reads , <EOL> input_left_all_map , <EOL> input_left_segments_maps ) = argv [ x : x + <NUM_LIT:8> ] <EOL> input_left_segments_maps = input_left_segments_maps . split ( "<STR_LIT:U+002C>" ) <EOL> if len ( argv ) > x + <NUM_LIT:8> : <EOL> ( input_right_all_reads , <EOL> input_right_all_map , <EOL> input_right_segments_maps ) = argv [ x + <NUM_LIT:8> : x + <NUM_LIT:11> ] <EOL> input_right_segments_maps = input_right_segments_maps . split ( "<STR_LIT:U+002C>" ) <EOL> else : <EOL> input_right_all_reads = "<STR_LIT>" <EOL> input_right_all_map = "<STR_LIT>" <EOL> input_right_segments_maps = [ ] <EOL> keys = set ( ) <EOL> files_to_split = set ( [ input_left_all_map , input_right_all_map ] + input_left_segments_maps + input_right_segments_maps ) <EOL> E . info ( "<STR_LIT>" % len ( files_to_split ) ) <EOL> for filename in files_to_split : <EOL> if filename == "<STR_LIT>" : continue <EOL> E . info ( "<STR_LIT>" % filename ) <EOL> base , ext = os . path . splitext ( filename ) <EOL> f = glob . glob ( "<STR_LIT>" % ( filename , ext ) ) <EOL> if f : <EOL> E . info ( "<STR_LIT>" ) <EOL> keys . update ( [ re . match ( "<STR_LIT>" % ( filename , ext ) , x ) . groups ( ) [ <NUM_LIT:0> ] for x in f ] ) <EOL> continue <EOL> infile = IOTools . openFile ( filename ) <EOL> outfiles = IOTools . FilePool ( filename + "<STR_LIT>" + ext ) <EOL> for line in infile : <EOL> key = line . split ( "<STR_LIT:\t>" ) [ <NUM_LIT:2> ] <EOL> keys . add ( key ) <EOL> outfiles . write ( key , line ) <EOL> outfiles . close ( ) <EOL> E . info ( "<STR_LIT>" % ( len ( keys ) , list ( keys ) ) ) <EOL> pool = multiprocessing . pool . ThreadPool ( options . nthreads ) <EOL> tmpdir = os . path . dirname ( input_left_all_reads ) <EOL> logdir = os . path . join ( tmpdir [ : - len ( "<STR_LIT>" ) ] , "<STR_LIT>" ) <EOL> if not os . path . exists ( logdir ) : <EOL> raise IOError ( "<STR_LIT>" % logdir ) <EOL> args = [ ] <EOL> for key in keys : <EOL> def modout ( old , key ) : <EOL> if not old : return "<STR_LIT>" <EOL> _ , ext = os . path . splitext ( old ) <EOL> return old + "<STR_LIT>" % ( key , ext ) <EOL> def modin ( old , key ) : <EOL> if not old : return "<STR_LIT>" <EOL> _ , ext = os . path . splitext ( old ) <EOL> return old + "<STR_LIT>" % ( key , ext ) <EOL> def modgenome ( old , key ) : <EOL> dirname , filename = os . path . split ( old ) <EOL> genome , ext = os . path . splitext ( filename ) <EOL> if genome . lower ( ) . endswith ( "<STR_LIT>" ) : genome = genome [ : - <NUM_LIT:3> ] <EOL> new = os . path . join ( dirname , genome + "<STR_LIT>" , key + ext ) <EOL> if not os . path . exists ( new ) : <EOL> raise ValueError ( "<STR_LIT>" % new ) <EOL> return new <EOL> cmd = [ "<STR_LIT>" ] + all_options + [ input_missing_reads , modgenome ( input_genome , key ) , modout ( output_junctions , key ) , modout ( output_insertions , key ) , modout ( output_deletions , key ) , input_left_all_reads , modin ( input_left_all_map , key ) , "<STR_LIT:U+002C>" . join ( [ modin ( x , key ) for x in input_left_segments_maps ] ) , input_right_all_reads , modin ( input_right_all_map , key ) , "<STR_LIT:U+002C>" . join ( [ modin ( x , key ) for x in input_right_segments_maps ] ) ] <EOL> logfile = os . path . join ( logdir , "<STR_LIT>" % key ) <EOL> args . append ( ( cmd , logfile ) ) <EOL> E . info ( "<STR_LIT>" % len ( keys ) ) <EOL> pool . map ( runCommand , args , chunksize = <NUM_LIT:1> ) <EOL> pool . close ( ) <EOL> pool . join ( ) <EOL> E . info ( "<STR_LIT>" ) <EOL> E . info ( "<STR_LIT>" ) <EOL> for filename in ( output_junctions , output_insertions , output_deletions ) : <EOL> outfile = open ( filename , "<STR_LIT:w>" ) <EOL> for inf in glob . glob ( filename + "<STR_LIT>" ) : <EOL> infile = open ( inf , "<STR_LIT:r>" ) <EOL> outfile . write ( infile . read ( ) ) <EOL> infile . close ( ) <EOL> outfile . close ( ) <EOL> E . info ( "<STR_LIT>" ) <EOL> E . info ( "<STR_LIT>" ) <EOL> for f in glob . glob ( os . path . join ( tmpdir , "<STR_LIT>" ) ) + glob . glob ( os . path . join ( tmpdir , "<STR_LIT>" ) ) : <EOL> os . remove ( f ) <EOL> E . Stop ( ) <EOL> if __name__ == "<STR_LIT:__main__>" : <EOL> sys . exit ( main ( sys . argv ) ) </s>
