--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/removeFastaSubSequence.py	Wed Aug 02 18:09:53 2017 -0400
@@ -0,0 +1,42 @@
+
+# This program checks if any of the sequence in a query fasta file is present in the 
+# reference fasta file (checks for sub-string) or not. If they are present, it removes it.
+# The updated database will have sequences unique to query fasta file.
+
+def main():
+    import sys
+    from Bio import SeqIO
+    
+    ref_fastaFile = sys.argv[1].strip()
+    query_fastaFile = sys.argv[2].strip()
+    
+    x = SeqIO.to_dict(SeqIO.parse(ref_fastaFile, "fasta"))
+    y = x.values()
+    b = []
+    for a in y:
+        b.append(str(a.seq))
+    ref_fastaSeq = "#".join(b)
+    
+    outfh = open(sys.argv[3].strip(), "w")
+    
+    x = SeqIO.to_dict(SeqIO.parse(query_fastaFile, "fasta"))
+    y = x.values()
+    count = 0
+    for a in x.keys():
+        seq = str(x[a].seq)
+        desc = str(x[a].description)
+        if ref_fastaSeq.find(seq) < 0:
+            outfh.write(">" + desc + "\n" + seq + "\n")
+        else:
+            count = count + 1
+    print >> sys.stdout,"Total Number of Sequences Removed: %d" % count
+    outfh.close()
+    return None
+
+if __name__ == "__main__":
+    main()
+    
+    
+    
+
+