view ccat_wrapper.py @ 9:bd9147788dd5 draft

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#!/usr/bin/env python

import sys, subprocess, tempfile, shutil, os.path

def get_top_count( filename ):
    for line in open( filename ):
        if line.startswith( 'outputNum' ):
            return int( line.split()[-1].strip() ) 

def stop_err( tmp_dir, exception ):
    print >> sys.stderr, "Error running CCAT."
    shutil.rmtree( tmp_dir ) #some error has occurred, provide info and remove possibly non-empty temp directory
    raise exception

def main():
    CCAT_BINARY = "/usr/bin/ccat/CCAT3.0/bin/CCAT"
    input_tag_file = sys.argv[1]
    input_control_file = sys.argv[2]
    genome = sys.argv[3]
    input_config_file = sys.argv[4]
    project_name = sys.argv[5]
    output_peak_file = sys.argv[6]
    output_region_file = sys.argv[7]
    output_top_file = sys.argv[8]
    output_log_file = sys.argv[9]
    root_dir = sys.argv[10]
    
    ###### CREATE ANNOTATION FILES #########
    databasePath = root_dir+"/database/files"
    
    subprocess.Popen('mkdir -p '+databasePath+'/nebulaAnnotations', shell=True)
    subprocess.Popen('mkdir -p '+databasePath+'/nebulaAnnotations/'+genome, shell=True)

    nebulaGenomePath=databasePath+"/nebulaAnnotations/"+genome

    FAIFILE='n'
    LENFILE='n'
    DICTFILE='n'
    CHROFILE='n'
    MAPFILE='n'
    
    if not os.path.isfile(nebulaGenomePath+"/"+genome+".len"):
        FAIFILE='y'
        LENFILE='y'
        
    FILEPATH=databasePath.replace("database/files","tool-data")

    cmd='bash /usr/bin/create_annotation_files.sh '+FAIFILE+" "+LENFILE+" "+DICTFILE+" "+CHROFILE+" "+FILEPATH+" "+genome+" "+MAPFILE+" "+nebulaGenomePath
    process=subprocess.Popen(cmd, shell=True)
    process.wait()

    chrom_info_file=nebulaGenomePath+"/"+genome+".len"
    
    tmp_dir = tempfile.mkdtemp()
    try:
        proc = subprocess.Popen( args="%s %s > %s" % ( CCAT_BINARY, " ".join( map( lambda x: "%s" % x, [ input_tag_file, input_control_file, chrom_info_file, input_config_file, project_name ] ) ), output_log_file ), shell=True, cwd=tmp_dir )
        proc.wait()
        if proc.returncode:
            raise Exception( "Error code: %i" % proc.returncode )
        output_num = get_top_count( input_config_file )
        shutil.move( os.path.join( tmp_dir, "%s.significant.peak" % project_name ), output_peak_file )
        shutil.move( os.path.join( tmp_dir, "%s.significant.region" % project_name ), output_region_file )
        shutil.move( os.path.join( tmp_dir, "%s.top%i.peak" % ( project_name, output_num ) ), output_top_file )
    except Exception, e:
        return stop_err( tmp_dir, e )
    os.rmdir( tmp_dir ) #clean up empty temp working directory

if __name__ == "__main__": main()