--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fasta_tabular_converter.py	Sun Jun 21 14:28:49 2015 -0400
@@ -0,0 +1,88 @@
+#!/usr/bin/python
+#
+import sys
+from collections import defaultdict
+
+def readfasta_writetabular(fasta, tabular):
+  F = open(fasta, "r")
+  for line in F:
+    if line[0] == ">": continue
+    else:
+      seqdic[line[:-1]] += 1
+  F.close()
+  F = open(tabular, "w")
+  for seq in sorted(seqdic, key=seqdic.get, reverse=True):
+    print >> F, "%s\t%s" % (seq, seqdic[seq])
+  F.close()
+    
+        
+def readtabular_writefasta(tabular, fasta):
+  F = open(tabular, "r")
+  Fw = open(fasta, "w")
+  counter = 0
+  for line in F:
+    fields = line.split()
+    for i in range(int(fields[1])):
+      counter += 1
+      print >> Fw, ">%s\n%s" % (counter, fields[0])
+  F.close()
+  Fw.close()
+
+def readtabular_writefastaweighted (tabular, fasta):
+  F = open(tabular, "r")
+  Fw = open(fasta, "w")
+  counter = 0
+  for line in F:
+    counter += 1
+    fields = line[:-1].split()
+    print >> Fw, ">%s_%s\n%s" % (counter, fields[1],  fields[0])
+  F.close()
+  Fw.close()
+
+def readfastaeighted_writefastaweighted(fastaweigthed_input, fastaweigthed_reparsed):
+  F = open(fastaweigthed_input, "r")
+  number_reads = 0
+  for line in F:
+    if line[0] == ">":
+      weigth = int(line[1:-1].split("_")[-1])
+      number_reads += weigth
+    else:
+      seqdic[line[:-1]] += weigth
+  F.close()
+  F = open(fastaweigthed_reparsed, "w")
+  n=0
+  for seq in sorted(seqdic, key=seqdic.get, reverse=True):
+    n += 1
+    print >> F, ">%s_%s\n%s" % (n, seqdic[seq], seq)
+  F.close()
+  print "%s reads collapsed" % number_reads
+
+def readfastaeighted_writefasta(fastaweigthed, fasta):
+  F = open(fastaweigthed, "r")
+  Fw = open(fasta, "w")
+  counter = 0
+  for line in F:
+    if line[0] == ">":
+      weigth = int(line[1:-1].split("_")[-1])
+    else:
+      seq = line[:-1]
+      for i in range (weigth):
+        counter += 1
+        print >> Fw, ">%s\n%s" % (counter, seq)
+  F.close()
+  Fw.close()
+
+
+seqdic = defaultdict(int)
+option = sys.argv[3]
+
+if option == "fasta2tabular":
+  readfasta_writetabular(sys.argv[1], sys.argv[2])
+elif option == "tabular2fasta":
+  readtabular_writefasta(sys.argv[1], sys.argv[2])
+elif option == "tabular2fastaweight":
+  readtabular_writefastaweighted (sys.argv[1], sys.argv[2])
+elif option == "fastaweight2fastaweight":
+  readfastaeighted_writefastaweighted(sys.argv[1], sys.argv[2])
+elif option == "fastaweight2fasta":
+  readfastaeighted_writefasta(sys.argv[1], sys.argv[2])