--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/tools/blast2align.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,75 @@
+#!/usr/bin/env python
+
+import sys
+import getopt
+
+
+def help():
+    print
+    print "usage: blast2align.py [ options ]"
+    print "options:"
+    print "     -h: this help"
+    print "     -i: input file name (format=tabulated BLAST)"
+    print "     -o: output file name (format=align, default=inFileName+'.align')"
+    print
+
+
+def blast2align( inFile, outFile ):
+    inFileHandler = open( inFile, "r" )
+    outFileHandler = open( outFile, "w" )
+    while True:
+        line = inFileHandler.readline()
+        if line == "":
+            break
+        if line[0] != "#":
+            data = line.split("\t")
+            qryName = data[0]
+            sbjName = data[1]
+            percId = data[2]
+            qryStart = data[6]
+            qryEnd = data[7]
+            sbjStart = data[8]
+            sbjEnd = data[9]
+            Eval = data[10]
+            bitScore = data[11][:-1]
+            string = "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % ( qryName, qryStart, qryEnd, sbjName, sbjStart, sbjEnd, Eval, bitScore, percId )
+            outFileHandler.write( string )
+    inFileHandler.close()
+    outFileHandler.close()
+    
+    
+def main():
+    inFileName = ""
+    outFileName = ""
+
+    try:
+        opts, args = getopt.getopt(sys.argv[1:],"hi:o:")
+    except getopt.GetoptError, err:
+        sys.stderr.write( "%s\n" % str(err) )
+        help()
+        sys.exit(1)
+    for o,a in opts:
+        if o == "-h":
+            help()
+            sys.exit(0)
+        elif o == "-i":
+            inFileName = a
+        elif o == "-o":
+            outFileName = a
+  
+    if  inFileName == "":
+        msg =  "ERROR: missing input file name (-i)"
+        sys.stderr.write( "%s\n" % msg )
+        help()
+        sys.exit(1)
+
+    if outFileName == "":
+        outFileName = inFileName + ".align"
+
+    blast2align( inFileName, outFileName )
+
+    return 0
+
+
+if __name__ == "__main__":
+    main()