changeset 6:a4f0a7862da6 draft

Deleted selected files

--- a/spp_wrapper.py	Fri Jan 18 18:41:08 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,100 +0,0 @@
-#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]
-
-    #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 /mnt/galaxyTools/galaxy-central/tools/modENCODE_DCC_tools/spp/run_spp.R -c=%s" % ( 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 )
-
-    #test = "%s_VS_%s.narrowPeak.gz" %(chip_name, input_name)
-    #print test
-    #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()