bug 1 base

bin/insilicoRRBSdigestion.py

@@ -37,7 +37,6 @@ import seqio as seqio
 GRAPH_CLASS_PARTITION = 100
 MAX_FRAGMENT_LEN_IN_HISTOGRAM = 5000
 ENZYME_PATH=os.path.join(os.path.dirname(os.path.realpath(__file__)),"..","lib","enzyme.txt")
-
 def version_string ():
     """
     Return the insilicoRRBSdigestion version
@@ -261,7 +260,7 @@ def compute_fragment_size_per_range(ranges,fragments_length):
        ranges[key]["size"]=0
    for i in fragments_length :
        for key in ranges.keys():
-           if i>=ranges[key]["coord"][0] and i<ranges[key]["coord"][1] :
+           if i>=ranges[key]["coord"][0] and i<=ranges[key]["coord"][1] :
                ranges[key]["nb_fragment"]+=1
                ranges[key]["size"]+=i
                break
@@ -269,14 +268,12 @@ def compute_fragment_size_per_range(ranges,fragments_length):
 if __name__ == "__main__":
 
     # Get available enzyme
-    
     all_enzymes = {'None':0}
     if os.path.exists(ENZYME_PATH) :
         all_enzymes = get_available_enzymes(ENZYME_PATH)
-    
     parser = OptionParser(usage="Usage: insilicoRRBS.py -i FILE [options]")
 
-    usage = "usage: %prog -i file.fa -o output.stats -c CpGisland.bed"
+    usage = "usage: %prog -i file.fa -o output_directory -c file.bed"
     desc = "The script simulates a complete enzymatic digestion of the genome to\
             identify all the potential restriction fragments. Then, for each size\
             range (from min to max fragment length of bins size ) it computes different metrics"