changeset 9:bd9147788dd5 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ccat_wrapper.py	Thu Jan 21 09:47:12 2016 -0500
@@ -0,0 +1,68 @@
+#!/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()