--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/blastx_to_scaffold.py	Sun Jun 21 14:40:10 2015 -0400
@@ -0,0 +1,66 @@
+#!/usr/bin/python
+import sys
+import argparse
+
+def insert_newlines(string, every=60):
+    lines = []
+    for i in xrange(0, len(string), every):
+        lines.append(string[i:i+every])
+    return '\n'.join(lines)
+    
+def Parser():
+    the_parser = argparse.ArgumentParser(
+        description="Generate DNA scaffold from blastx alignment of Contigs")
+    the_parser.add_argument(
+        '--sequences', action="store", type=str, help="input sequence file in fasta format")
+    the_parser.add_argument(
+        '--blastx-tab', dest="blastx_tab", action="store", type=str, help="13-columns tabular blastx output")
+    the_parser.add_argument(
+        '--output', action="store", type=str, help="output file path, fasta format")
+    args = the_parser.parse_args()
+    return args
+
+def __main__():
+    args = Parser()
+    protLenght = int (open (args.blastx_tab, "r").readline().split("\t")[12])
+    BlastxOutput = open (args.blastx_tab, "r")
+    Contigs = open (args.sequences, "r")
+    ContigsDict = {}
+    protScaffold = {}
+    
+    for line in Contigs:
+        if line[0] == ">":
+            header = line[1:-1]
+            ContigsDict[header] = ""
+        else:
+            ContigsDict[header] += line[:-1]
+            
+    protScaffold = dict ( [(i,"NNN") for i in range (1, protLenght+1)] )
+        
+    for line in BlastxOutput:
+        fields = line[:-1].split("\t")
+        queryStart = int(fields[6])
+        queryStop = int(fields[7])
+        subjectStart = int(fields[8])
+        subjectStop = int(fields[9])
+        seqHeader = fields[0]
+        sequence = ContigsDict[seqHeader]
+        for i in range (subjectStart, subjectStop):
+            del protScaffold[i]
+        protScaffold[subjectStop] = ContigsDict[seqHeader][queryStart -1: queryStop]
+        
+    finalSeqList = []
+    for i in sorted (protScaffold):
+        finalSeqList.append(protScaffold[i])
+    finalSequence = insert_newlines("".join(finalSeqList))
+     
+    Out = open (args.output, "w")
+    print >> Out, ">Scaffold"
+    print >> Out, finalSequence
+            
+    BlastxOutput.close()
+    Contigs.close()
+    Out.close()
+        
+if __name__ == "__main__":
+    __main__()