Mercurial > repos > devteam > ccat
comparison ccat_wrapper.py @ 0:a0c8dc671a23 draft
Imported from capsule None
| author | devteam |
|---|---|
| date | Mon, 27 Jan 2014 09:27:03 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:a0c8dc671a23 |
|---|---|
| 1 import sys, subprocess, tempfile, shutil, os.path | |
| 2 | |
| 3 CCAT_BINARY = "CCAT" | |
| 4 | |
| 5 def get_top_count( filename ): | |
| 6 for line in open( filename ): | |
| 7 if line.startswith( 'outputNum' ): | |
| 8 return int( line.split()[-1].strip() ) | |
| 9 | |
| 10 def stop_err( tmp_dir, exception ): | |
| 11 print >> sys.stderr, "Error running CCAT." | |
| 12 shutil.rmtree( tmp_dir ) #some error has occurred, provide info and remove possibly non-empty temp directory | |
| 13 raise exception | |
| 14 | |
| 15 def main(): | |
| 16 input_tag_file = sys.argv[1] | |
| 17 input_control_file = sys.argv[2] | |
| 18 chrom_info_file = sys.argv[3] | |
| 19 input_config_file = sys.argv[4] | |
| 20 project_name = sys.argv[5] | |
| 21 output_peak_file = sys.argv[6] | |
| 22 output_region_file = sys.argv[7] | |
| 23 output_top_file = sys.argv[8] | |
| 24 output_log_file = sys.argv[9] | |
| 25 | |
| 26 tmp_dir = tempfile.mkdtemp() | |
| 27 try: | |
| 28 assert os.path.exists( chrom_info_file ), "The required chromosome length file does not exist." | |
| 29 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 ) | |
| 30 proc.wait() | |
| 31 if proc.returncode: | |
| 32 raise Exception( "Error code: %i" % proc.returncode ) | |
| 33 output_num = get_top_count( input_config_file ) | |
| 34 shutil.move( os.path.join( tmp_dir, "%s.significant.peak" % project_name ), output_peak_file ) | |
| 35 shutil.move( os.path.join( tmp_dir, "%s.significant.region" % project_name ), output_region_file ) | |
| 36 shutil.move( os.path.join( tmp_dir, "%s.top%i.peak" % ( project_name, output_num ) ), output_top_file ) | |
| 37 except Exception, e: | |
| 38 return stop_err( tmp_dir, e ) | |
| 39 os.rmdir( tmp_dir ) #clean up empty temp working directory | |
| 40 | |
| 41 if __name__ == "__main__": main() |