changeset 1:288ae929e6b9 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spp_wrapper.py	Tue Dec 18 10:45:06 2012 -0500
@@ -0,0 +1,99 @@
+#purpose: python wrapper to run spp
+#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
+
+def main():
+    options = simplejson.load( open( sys.argv[1] ) )
+    output_narrow_peak = sys.argv[2]
+    output_region_peak = sys.argv[3]
+    output_peakshift_file = sys.argv[4]
+    output_rdata_file = sys.argv[5]
+    output_plot_file = sys.argv[6]
+    output_default_file = sys.argv[7]
+    script_path = sys.argv[8]
+
+    #set file extensions and set mandatory options
+    #========================================================================================    
+    experiment_name = '_'.join( options['experiment_name'].split() ) #save experiment name
+
+    chip_file = "%s.bam" % (options['chip_file'])
+    subprocess.call(["cp", options['chip_file'], chip_file])
+
+    cmdline = "Rscript %s/run_spp.R -c=%s" % (script_path, chip_file )
+    if 'input_file' in options:
+        input_file = "%s.bam" % (options['input_file'])
+        subprocess.call(["cp", options['input_file'], input_file])
+        cmdline = "%s -i=%s" % ( cmdline, input_file )
+
+    #set additional options
+    #========================================================================================
+    if (options['action'] == "cross_correlation"):
+	cmdline = "%s %s %s %s > default_output.txt" % ( cmdline, options['savp'], options['out'], options['rf'] ) 
+    elif (options['action'] == "peak_calling"):
+	cmdline = "%s -fdr=%s -npeak=%s %s %s %s %s %s > default_output.txt" % ( cmdline, options['fdr'], options['npeak'], options['savr'], options['savd'], options['savn'], options['savp'], options['rf'] ) 
+    elif (options['action'] == "idr"):
+	cmdline = "%s -npeak=%s %s %s %s %s > default_output.txt" % ( cmdline, options['npeak'], options['savr'], options['savp'], options['out'], options['rf'] ) 
+    elif (options['action'] == "custom"):
+	cmdline = "%s -s=%s %s -x=%s -fdr=%s -npeak=%s %s %s" % ( cmdline, options['s'], options['speak'], options['x'], options['fdr'], options['npeak'], options['filtchr'], options['rf'] )
+	cmdline = "%s %s  %s %s %s %s > default_output.txt" % ( cmdline, options['out'], options['savn'], options['savr'], options['savp'], options['savd'] )
+
+    #run cmdline
+    #========================================================================================
+    tmp_dir = tempfile.mkdtemp()
+    stderr_name = tempfile.NamedTemporaryFile().name
+    proc = subprocess.Popen( args=cmdline, shell=True, cwd=tmp_dir, stderr=open( stderr_name, 'wb' ) )
+    proc.wait()
+
+    #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 )
+
+
+    #determine if the outputs are there, copy them to the appropriate dir and filename
+    #========================================================================================
+    created_default_file =  os.path.join( tmp_dir, "default_output.txt" )
+    if os.path.exists( created_default_file ):
+        shutil.move( created_default_file, output_default_file )
+
+    chip_name = os.path.basename(options['chip_file'])
+    input_name = os.path.basename(options['input_file'])
+    created_narrow_peak =  os.path.join( "/mnt/galaxyData/files/000", "%s_VS_%s.narrowPeak.gz" % (chip_name, input_name) )
+    if os.path.exists( created_narrow_peak ):
+        shutil.move( created_narrow_peak, output_narrow_peak )
+ 
+    created_region_peak =  os.path.join( "/mnt/galaxyData/files/000", "%s_VS_%s.regionPeak.gz" % (chip_name, input_name) )
+    if os.path.exists( created_region_peak ):
+        shutil.move( created_region_peak, output_region_peak )
+
+    created_peakshift_file =  os.path.join( tmp_dir, "peakshift.txt" )
+    if os.path.exists( created_peakshift_file ):
+        shutil.move( created_peakshift_file, output_peakshift_file )
+
+    created_rdata_file =  os.path.join( tmp_dir, "%s.Rdata" % options['chip_file'] )
+    if os.path.exists( created_rdata_file ):
+        shutil.move( created_rdata_file, output_rdata_file )
+
+    created_plot_file =  os.path.join( tmp_dir, "%s.pdf" % options['chip_file'] )
+    if os.path.exists( created_plot_file ):
+        shutil.move( created_plot_file, output_plot_file )
+
+    
+    os.unlink( stderr_name )
+    #os.rmdir( tmp_dir )
+
+if __name__ == "__main__": main()