diff cuffdiff_wrapper.py @ 2:fdf01b3c1841

Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output

--- a/cuffdiff_wrapper.py	Mon Feb 04 21:23:20 2013 -0600
+++ b/cuffdiff_wrapper.py	Fri Nov 08 14:54:01 2013 -0600
@@ -33,7 +33,7 @@
 
 def stop_err( msg ):
     sys.stderr.write( "%s\n" % msg )
-    sys.exit()
+    sys.exit(1)
     
 # Copied from sam_to_bam.py:
 def check_seq_file( dbkey, cached_seqs_pointer_file ):
@@ -62,6 +62,8 @@
     parser.add_option( '-c', '--min-alignment-count', dest='min_alignment_count', help='The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples. If no testing is performed, changes in the locus are deemed not signficant, and the locus\' observed changes don\'t contribute to correction for multiple testing. The default is 1,000 fragment alignments (up to 2,000 paired reads).' )
     parser.add_option( '--FDR', dest='FDR', help='The allowed false discovery rate. The default is 0.05.' )
     parser.add_option( '-u', '--multi-read-correct', dest='multi_read_correct', action="store_true", help='Tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome')
+    parser.add_option( '--library-norm-method', dest='library_norm_method' )
+    parser.add_option( '--dispersion-method', dest='dispersion_method' )
 
     # Advanced Options:	
     parser.add_option( '--num-importance-samples', dest='num_importance_samples', help='Sets the number of importance samples generated for each locus during abundance estimation. Default: 1000' )
@@ -98,12 +100,12 @@
     parser.add_option( "--genes_exp_output", dest="genes_exp_output" )
     parser.add_option( "--tss_groups_exp_output", dest="tss_groups_exp_output" )
     parser.add_option( "--cds_exp_fpkm_tracking_output", dest="cds_exp_fpkm_tracking_output" )
+    parser.add_option( "--cds_diff_output", dest="cds_diff_output" )
     parser.add_option( "--isoforms_count_tracking_output", dest="isoforms_count_tracking_output" )
     parser.add_option( "--genes_count_tracking_output", dest="genes_count_tracking_output" )
     parser.add_option( "--cds_count_tracking_output", dest="cds_count_tracking_output" )
     parser.add_option( "--tss_groups_count_tracking_output", dest="tss_groups_count_tracking_output" )
     parser.add_option( "--splicing_diff_output", dest="splicing_diff_output" )
-    parser.add_option( "--cds_diff_output", dest="cds_diff_output" )
     parser.add_option( "--promoters_diff_output", dest="promoters_diff_output" )
     parser.add_option( "--run_info_output", dest="run_info_output" )
     parser.add_option( "--read_groups_info_output", dest="read_groups_info_output" )
@@ -137,7 +139,6 @@
     if not os.path.exists( cuffdatadir ):
         os.makedirs( cuffdatadir )
     
-    
     # If doing bias correction, set/link to sequence file.
     if options.do_bias_correction:
         if options.ref_file != 'None':
@@ -162,6 +163,10 @@
     cmd = "cuffdiff --no-update-check -q"
     
     # Add options.
+    if options.library_norm_method:
+        cmd += ( " --library-norm-method %s" % options.library_norm_method )
+    if options.dispersion_method:
+        cmd += ( " --dispersion-method %s" % options.dispersion_method )
     if options.inner_dist_std_dev:
         cmd += ( " -s %i" % int ( options.inner_dist_std_dev ) )
     if options.num_threads:
@@ -188,7 +193,7 @@
     if options.groups:
         cmd += " --labels "
         for label in options.labels:
-            cmd += label + ","
+            cmd += '"%s",' % label
         cmd = cmd[:-1]
 
         cmd += " " + options.inputA + " "