--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macs2_wrapper.py	Fri Jan 18 09:47:22 2013 -0500
@@ -0,0 +1,177 @@
+#purpose: macs2 python wrapper
+#author: Ziru Zhou
+#date: November, 2012
+
+import sys, subprocess, tempfile, shutil, glob, os, os.path, gzip
+from galaxy import eggs
+import pkg_resources
+pkg_resources.require( "simplejson" )
+import simplejson
+
+CHUNK_SIZE = 1024
+
+#==========================================================================================
+#functions
+#==========================================================================================
+def gunzip_cat_glob_path( glob_path, target_filename, delete = False ):
+    out = open( target_filename, 'wb' )
+    for filename in glob.glob( glob_path ):
+        fh = gzip.open( filename, 'rb' )
+        while True:
+            data = fh.read( CHUNK_SIZE )
+            if data:
+                out.write( data )
+            else:
+                break
+        fh.close()
+        if delete:
+            os.unlink( filename )
+    out.close()
+
+def xls_to_interval( xls_file, interval_file, header = None ):
+    out = open( interval_file, 'wb' )
+    if header:
+        out.write( '#%s\n' % header )
+    wrote_header = False
+    #From macs readme: Coordinates in XLS is 1-based which is different with BED format.
+    for line in open( xls_file ):
+        #keep all existing comment lines
+        if line.startswith( '#' ):
+            out.write( line )
+	#added for macs2 since there is an extra newline 
+        elif line.startswith( '\n' ):
+            out.write( line )
+        elif not wrote_header:
+            out.write( '#%s' % line )
+	    print line
+            wrote_header = True
+        else:
+            fields = line.split( '\t' )
+            if len( fields ) > 1:
+                fields[1] = str( int( fields[1] ) - 1 )
+            out.write( '\t'.join( fields ) )
+    out.close()
+
+#==========================================================================================
+#main
+#==========================================================================================
+def main():
+    #take in options file and output file names
+    options = simplejson.load( open( sys.argv[1] ) )
+    outputs = simplejson.load( open( sys.argv[2] ) )
+
+    #=================================================================================
+    #parse options and execute macs2
+    #=================================================================================
+    #default inputs that are in every major command
+    experiment_name = '_'.join( options['experiment_name'].split() ) #save experiment name here, it will be used by macs for some file names
+    cmdline = "macs2 %s -t %s" % ( options['command'], ",".join( options['input_chipseq'] ) )
+    if options['input_control']:
+        cmdline = "%s -c %s" % ( cmdline, ",".join( options['input_control'] ) )
+
+    #=================================================================================
+    if (options['command'] == "callpeak"):
+    	output_bed = outputs['output_bed_file']
+    	output_extra_html = outputs['output_extra_file']
+    	output_extra_path = outputs['output_extra_file_path']
+    	output_peaks =  outputs['output_peaks_file']
+   	output_narrowpeaks = outputs['output_narrowpeaks_file']    
+	output_xls_to_interval_peaks_file = outputs['output_xls_to_interval_peaks_file']
+	output_xls_to_interval_negative_peaks_file = outputs['output_xls_to_interval_negative_peaks_file']
+
+	if 'pvalue' in options:
+    		cmdline = "%s --format='%s' --name='%s' --gsize='%s' --bw='%s' --pvalue='%s' --mfold %s %s %s %s" % ( cmdline, options['format'], experiment_name, options['gsize'], options['bw'], options['pvalue'], options['mfoldlo'], options['mfoldhi'], options['nolambda'], options['bdg'] )
+	elif 'qvalue' in options:
+    		cmdline = "%s --format='%s' --name='%s' --gsize='%s' --bw='%s' --qvalue='%s' --mfold %s %s %s %s" % ( cmdline, options['format'], experiment_name, options['gsize'], options['bw'], options['qvalue'], options['mfoldlo'], options['mfoldhi'], options['nolambda'], options['bdg'] )
+		
+	if 'nomodel' in options:
+        	cmdline = "%s --nomodel --shiftsize='%s'" % ( cmdline, options['nomodel'] )
+    #=================================================================================
+    if (options['command'] == "bdgcmp"):
+	output_bdgcmp = outputs['output_bdgcmp_file']
+
+	cmdline = "%s -m %s -p %s -o bdgcmp_out.bdg" % ( cmdline, options['m'], options['pseudocount'] )
+    #=================================================================================
+
+    tmp_dir = tempfile.mkdtemp() #macs makes very messy output, need to contain it into a temp dir, then provide to user
+    stderr_name = tempfile.NamedTemporaryFile().name # redirect stderr here, macs provides lots of info via stderr, make it into a report
+    proc = subprocess.Popen( args=cmdline, shell=True, cwd=tmp_dir, stderr=open( stderr_name, 'wb' ) )
+    proc.wait()
+    #We don't want to set tool run to error state if only warnings or info, e.g. mfold could be decreased to improve model, but let user view macs log
+    #Do not terminate if error code, allow dataset (e.g. log) creation and cleanup
+    if proc.returncode:
+        stderr_f = open( stderr_name )
+        while True:
+            chunk = stderr_f.read( CHUNK_SIZE )
+            if not chunk:
+                stderr_f.close()
+                break
+            sys.stderr.write( chunk )
+    
+    #=================================================================================
+    #copy files created by macs2 to appripriate directory with the provided names
+    #=================================================================================
+
+    #=================================================================================
+    #move files generated by callpeak command 
+    if (options['command'] == "callpeak"):
+    	#run R to create pdf from model script
+    	if os.path.exists( os.path.join( tmp_dir, "%s_model.r" % experiment_name ) ):
+     	   	cmdline = 'R --vanilla --slave < "%s_model.r" > "%s_model.r.log"' % ( experiment_name, experiment_name )
+     	   	proc = subprocess.Popen( args=cmdline, shell=True, cwd=tmp_dir )
+		proc.wait()
+        
+    	#move bed out to proper output file
+    	created_bed_name =  os.path.join( tmp_dir, "%s_peaks.bed" % experiment_name )
+    	if os.path.exists( created_bed_name ):
+        	shutil.move( created_bed_name, output_bed )
+
+    	#OICR peak_xls file
+    	created_peak_xls_file =  os.path.join( tmp_dir, "%s_peaks.xls" % experiment_name )
+    	if os.path.exists( created_peak_xls_file ):
+        	# shutil.copy( created_peak_xls_file, os.path.join ( "/mnt/galaxyData/tmp/", "%s_peaks.xls" % ( os.path.basename(output_extra_path) )))
+		shutil.copyfile( created_peak_xls_file, output_peaks )   
+
+    	#peaks.encodepeaks (narrowpeaks) file
+    	created_narrowpeak_file = os.path.join (tmp_dir, "%s_peaks.encodePeak" % experiment_name )
+    	if os.path.exists( created_narrowpeak_file ):
+		shutil.move (created_narrowpeak_file, output_narrowpeaks )
+
+ 	#parse xls files to interval files as needed
+   	#if 'xls_to_interval' in options:
+    	if (options['xls_to_interval'] == "True"):
+        	create_peak_xls_file = os.path.join( tmp_dir, '%s_peaks.xls' % experiment_name )
+        	if os.path.exists( create_peak_xls_file ):
+            		xls_to_interval( create_peak_xls_file, output_xls_to_interval_peaks_file, header = 'peaks file' )
+        	create_peak_xls_file = os.path.join( tmp_dir, '%s_negative_peaks.xls' % experiment_name )
+        	if os.path.exists( create_peak_xls_file ):
+			print "negative file exists"
+            		xls_to_interval( create_peak_xls_file, output_xls_to_interval_negative_peaks_file, header = 'negative peaks file' )
+
+    	#move all remaining files to extra files path of html file output to allow user download
+    	out_html = open( output_extra_html, 'wb' )
+    	out_html.write( '<html><head><title>Additional output created by MACS (%s)</title></head><body><h3>Additional Files:</h3><p><ul>\n' % experiment_name )
+    	os.mkdir( output_extra_path )
+    	for filename in sorted( os.listdir( tmp_dir ) ):
+    		shutil.move( os.path.join( tmp_dir, filename ), os.path.join( output_extra_path, filename ) )
+        	out_html.write( '<li><a href="%s">%s</a></li>\n' % ( filename, filename ) )
+		#out_html.write( '<li><a href="%s">%s</a>peakxls %s SomethingDifferent tmp_dir %s path %s exp_name %s</li>\n' % ( created_peak_xls_file, filename, filename, tmp_dir, output_extra_path, experiment_name ) )
+    	out_html.write( '</ul></p>\n' )
+    	out_html.write( '<h3>Messages from MACS:</h3>\n<p><pre>%s</pre></p>\n' % open( stderr_name, 'rb' ).read() )
+    	out_html.write( '</body></html>\n' )
+    	out_html.close()
+
+    #=================================================================================
+    #move files generated by bdgcmp command
+    if (options['command'] == "bdgcmp"):
+    	created_bdgcmp_file = os.path.join (tmp_dir, "bdgcmp_out.bdg" )
+    	if os.path.exists( created_bdgcmp_file ):
+		shutil.move (created_bdgcmp_file, output_bdgcmp )
+     
+    #=================================================================================    
+    #cleanup
+    #=================================================================================    
+    os.unlink( stderr_name )
+    os.rmdir( tmp_dir )
+
+if __name__ == "__main__": main()