diff ccat_wrapper.py @ 2:1a6979fbd544 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat commit 1370bb21ee5712a13a26d289065406c5d489b8cc"

--- a/ccat_wrapper.py	Tue Jul 21 14:13:34 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,41 +0,0 @@
-import sys, subprocess, tempfile, shutil, os.path
-
-CCAT_BINARY = "CCAT"
-
-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():
-    input_tag_file = sys.argv[1]
-    input_control_file = sys.argv[2]
-    chrom_info_file = 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]
-    
-    tmp_dir = tempfile.mkdtemp()
-    try:
-        assert os.path.exists( chrom_info_file ), "The required chromosome length file does not exist."
-        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()