diff rdpmulticlassifier/scripts/.svn/text-base/generateOTUtable.py.svn-base @ 0:a73ae72b47aa draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rdpmulticlassifier/scripts/.svn/text-base/generateOTUtable.py.svn-base	Thu May 29 02:27:56 2014 -0400
@@ -0,0 +1,34 @@
+# create OTU Table by merging pre otu table with taxonomy assign by
+# rdpmulticlassifier
+# Tab-separated fields:
+# 1=OTU Label, 2=Count, 3=Sequence, 4 and following=Assigned taxonomy by
+# RDP Multi Classifier
+
+import sys, os
+
+OTUtable = sys.argv[1]
+PreOTUtable = sys.argv[2]
+RdpTaxonomy = sys.argv[3]
+
+def merge(output, preotu, tax):
+    writeoutput = open(output, 'w')
+    lookup = {} 
+    with open(tax) as f:
+        for x in f:
+	    list = x.split('\t')
+            length = len(list)
+	    rest =''
+            for k in range(1, length):
+                item= list[k].replace(' ','') 
+                item= item.replace('\n','')
+            	rest = rest+ item + '\t'
+	    lookup[list[0]] = rest
+    with open(preotu) as f:
+	for x in f:
+	    columns = x.split('\t')
+            otu = columns[0].replace(' ','')         
+            taxonomy = lookup[otu]
+            line = x.replace('\n','')
+	    writeoutput.write(line+taxonomy+'\n')
+
+merge(OTUtable, PreOTUtable, RdpTaxonomy)