--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bin/last_wrapper.py	Thu Dec 19 10:24:45 2019 -0500
@@ -0,0 +1,50 @@
+#!/usr/bin/env python3
+'''
+wrapper for last program
+run last  with BlastTab+ output and return mgblast like formated output
+last BlastTab+ output column order:
+1 query name
+2 reference name
+3 percent identity
+4 alignment length
+5 mismatches
+6 gap opens
+7 query start
+8 query end
+9 reference start
+10 reference end
+11 e-value
+12 bitscore
+13 length of query
+14 length of reference sequence
+(accordin lastal manual - more column may be added in future)
+
+Needed mgblast order:
+
+qseqid   1 -> 1
+qlen     2 -> 13
+qstart   3 -> 7
+qend     4 -> 8
+sseqid   5 -> 2
+slen     6 -> 14
+sstart   7 -> 9
+send     8 -> 10
+pident   9 -> 3
+bitscore 10-> 12
+evalue   11-> 11
+sstrand  12-> must be evaluated!
+
+'''
+import subprocess
+import sys
+last_command = " ".join(["lastal"] + sys.argv[1:])
+p = subprocess.Popen(last_command, shell=True, stdout=subprocess.PIPE)
+for j in p.stdout:
+    line = j.decode()
+    if line[0] != "#":
+        items = line.split("\t")
+        strand = "+" if int(items[6]) < int(items[7]) else "-"
+        out = "\t".join([items[i - 1]
+                         for i in [1, 13, 7, 8, 2, 14, 9, 10, 3, 12, 11]
+                         ]) + "\t" + strand + "\n"
+        print(out, end="")