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Hanfei Sun committed c1ee195

Modify config file

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Files changed (2)

 # gfold <= tophat
 # cufflinks <= tophat
 # summary_rpkm <= cufflinks
-# summary_mapping <= tophat
+# summary_mappped <= tophat
 # bam2bed <=tophat
 
-
+# a complete step order may be like the following
+# steps = fastqc_mapped,tophat,fastqc_mapped,summary_mapped,gfold,cufflinks,summary_rpkm
 steps = summary_mapping
 
 
 #! /usr/bin/env python
-# Time-stamp: <2011-11-17 18:40:10 sunhf>
+# Time-stamp: <2011-11-17 21:28:05 sunhf>
 """Rnaseq pipeline main script
 
 Copyright (c) 2011 Hanfei Sun <hfsun.tju@gmail.com>
         ModuleBase.__init__(self, name="Make the graph of evenness for quality control",conf=conf)
         # Evenness hasn't supported multi process yet
         self.tag2bam = lambda tag:self.find_path(conf['output.outputdir'], tag, source,"accepted_hits.bam")
-        self.tag2dir = lambda tag:self.find_path(conf['output.outputdir'], tag,"Summary_mapping")
+        self.tag2dir = lambda tag:self.find_path(conf['output.outputdir'], tag,"Summary_mappped")
         self.tag2even = lambda tag:self.tag2dir(tag)+"/"+tag
         self.tag2rscript = lambda tag:self.tag2even(tag)+".r"
         
                           m=re.search(r">>Per sequence quality scores.+?Count\n(.+?)\n>>END",t,re.S)
                           
 alias_dict=dict(fastqc_raw=FastqcRaw, fastqc_mapped=FastqcMapped,tophat=Tophat, cufflinks=Cufflinks,
-                gfold=gfold, bam2bed= Bam2Bed, summary_mapping= Summary_tophat,
+                gfold=gfold, bam2bed= Bam2Bed, summary_mapped= Summary_tophat,
                 summary_rpkm=Summary_cufflinks, summary_naiveqc= Summary_Fastqc)
 def read_config(configFile):
     """Read configuration file and parse it into a dictionary.