Mercurial > repos > john-mccallum > ssr_marker_design

view MISA/design_MISA.sh @ 0:3006582bfc76

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded V1.0 MISA tools and helper scripts
author john-mccallum
date Wed, 14 Sep 2011 23:57:57 -0400
parents
children
line wrap: on
line source

#!/bin/sh
#design primer sets from MISA output using Primer 3 and MISA helper scripts
#USAGE sh design_MISA.sh <misa_file> <source_fasta_file> <output_file>

#get directory
SCRIPT=`readlink -f $0`
SCRIPTPATH=`dirname $SCRIPT`

perl $SCRIPTPATH/p3_in.pl  $1 $2  temp.p3in

cat  temp.p3in | primer3_core  >  temp.p3out


perl $SCRIPTPATH/p3_out.pl  temp.p3out $1  $3

rm -f temp.*