diff cufflinks_wrapper.py @ 5:261425bba55d draft

corrected syntax error in wrapper.py

--- a/cufflinks_wrapper.py	Fri Aug 01 08:50:29 2014 -0400
+++ b/cufflinks_wrapper.py	Fri Aug 01 08:54:01 2014 -0400
@@ -21,7 +21,7 @@
     parser.add_option( '-G', '--GTF', dest='GTF', help='Tells Cufflinks to use the supplied reference annotation to estimate isoform expression. It will not assemble novel transcripts, and the program will ignore alignments not structurally compatible with any reference transcript.' )
     parser.add_option ("--compatible-hits-norm",dest='compatible_hits_norm',help='Count hits compatible with reference RNAs only')
     parser.add_option( '-g', '--GTF-guide', dest='GTFguide', help='use reference transcript annotation to guide assembly' )
-    parser.add_option("--3-overhang-tolerance",dest='3_overhang_tolerance', help='The number of bp allowed to overhang the 3prime end of a reference transcript when determining if an assembled transcript should be merged with it (ie, the assembled transcript is not novel). The default is 600 bp.')
+    parser.add_option("--3-overhang-tolerance",dest='three_overhang_tolerance', help='The number of bp allowed to overhang the 3prime end of a reference transcript when determining if an assembled transcript should be merged with it (ie, the assembled transcript is not novel). The default is 600 bp.')
     parser.add_option("--intron-overhang-tolerance",dest='intron_overhang_tolerance',help='The number of bp allowed to enter the intron of a reference transcript when determining if an assembled transcript should be merged with it (ie, the assembled transcript is not novel). The default is 50 bp.')
     parser.add_option("--no-faux-reads", dest='no_faux_reads',help='This option disables tiling of the reference transcripts with faux reads. Use this if you only want to use sequencing reads in assembly but do not want to output assembled transcripts that lay within reference transcripts. All reference transcripts in the input annotation will also be included in the output.')
     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')
@@ -54,8 +54,8 @@
     parser.add_option( '--max-bundle-length', dest='max_bundle_length', help='Maximum genomic length of a given bundle" help="Default: 3,500,000bp' )
     parser.add_option( '--max-bundle-frags', dest='max_bundle_frags', help='Sets the maximum number of fragments a locus may have before being skipped. Skipped loci are listed in skipped.gtf. Default: 1,000,000' )
     parser.add_option( '--min-intron-length', dest='min_intron_length', help='Minimal allowed intron size. Default: 50' )
-    parser.add_option( '--trim-3-avgcov-thresh', dest='trim_3_avgcov_thresh', help='Minimum average coverage required to attempt 3prime trimming. Default: 10' )
-    parser.add_option( '--trim-3-dropoff-frac', dest='trim_3_dropoff_frac', help='The fraction of average coverage below which to trim the 3prime end of an assembled transcript. Default: 0.1' )
+    parser.add_option( '--trim-3-avgcov-thresh', dest='trim_three_avgcov_thresh', help='Minimum average coverage required to attempt 3prime trimming. Default: 10' )
+    parser.add_option( '--trim-3-dropoff-frac', dest='trim_three_dropoff_frac', help='The fraction of average coverage below which to trim the 3prime end of an assembled transcript. Default: 0.1' )
 
 
     # Bias correction options.
@@ -119,7 +119,7 @@
 	cmd += ( " --compatible-hits-norm" )
     if options.GTFguide:
         cmd += ( " -g %s" % options.GTFguide )
-	cmd += ( " --3-overhang-tolerance %i" % int ( options.3_overhang_tolerance ) )
+	cmd += ( " --3-overhang-tolerance %i" % int ( options.three_overhang_tolerance ) )
 	cmd += ( " --intron-overhang-tolerance %i" % int ( options.intron_overhang_tolerance ) )
     if options.no_faux_reads:
 	cmd += ( " --no-faux-reads" )
@@ -148,10 +148,10 @@
 	cmd += ( " --max-bundle-frags %i" % int ( options.max_bundle_frags ) )
     if options.min_intron_length:
 	cmd += ( " --min-intron-length %i" % int ( options.min_intron_length ) )
-    if options.trim_3_avgcov_thresh:
-	cmd += ( " --trim-3-avgcov-thresh %i" % int ( options.trim_3_avgcov_thresh ) ) 
-    if options.trim_3_dropoff_frac:
-	cmd += ( " --trim-3-dropoff-frac %f" % float ( options.trim_3_dropoff_frac ) ) 
+    if options.trim_three_avgcov_thresh:
+	cmd += ( " --trim-3-avgcov-thresh %i" % int ( options.trim_three_avgcov_thresh ) ) 
+    if options.trim_three_dropoff_frac:
+	cmd += ( " --trim-3-dropoff-frac %f" % float ( options.trim_three_dropoff_frac ) ) 
 
     if options.do_bias_correction:
         cmd += ( " -b %s" % seq_path )