diff usearch_map_reads_to_otu/scripts/otu_table_transform.py @ 0:c10d09023766 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/usearch_map_reads_to_otu/scripts/otu_table_transform.py	Thu May 29 00:51:18 2014 -0400
@@ -0,0 +1,33 @@
+import sys, os
+#sys.path.insert(0, 'scripts');
+import parseFasta
+
+# Create OTU Table
+# OTU_Lable | Count | Sequence
+# 
+# Author: Anne Kunert
+#
+
+OTUmap = sys.argv[1]
+OTUcount = sys.argv[2]
+
+def transform(file):
+  seq = parseFasta.FastaParser(OTUmap)
+  with open(file) as f:
+    lis=[x.split() for x in f]
+  end=""
+  line=""
+  myseq=""
+  for x in zip(*lis):
+    otu_lable = x[0]
+    for item in seq:
+      if item == otu_lable:
+        myseq = seq.records[item]['sequence']
+        myseq = myseq.replace('\n','')
+    for y in x:
+      line= line+str(y)+"\t"
+    print(line+"\t"+myseq)
+    line=""
+    myseq=""
+#
+transform(OTUcount)