--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rgenetics/rgClustalw.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,60 @@
+"""
+rgclustalw.py
+wrapper for clustalw necessitated by bad choice of output path for .dnd file based on input file. Naughty.
+Copyright ross lazarus march 2011
+All rights reserved
+Licensed under the LGPL
+"""
+
+import sys,optparse,os,subprocess,tempfile,shutil
+
+class Clustrunner:
+    """
+    """
+    def __init__(self,opts=None):
+        self.opts = opts
+        self.iname = 'infile_copy'
+        shutil.copy(self.opts.input,self.iname) 
+
+    def run(self):
+        tlf = open(self.opts.outlog,'w')
+        cl = ['clustalw2 -INFILE=%s -OUTFILE=%s -OUTORDER=%s -TYPE=%s -OUTPUT=%s' % (self.iname,self.opts.output,self.opts.out_order,self.opts.dnarna,self.opts.outform)]
+        if self.opts.seq_range_end <> None and self.opts.seq_range_start <> None:
+            cl.append('-RANGE=%s,%s' % (self.opts.seq_range_start,self.opts.seq_range_end))
+        if self.opts.outform=='CLUSTAL' and self.opts.outseqnos <> None:
+            cl.append('-SEQNOS=ON')
+        process = subprocess.Popen(' '.join(cl), shell=True, stderr=tlf, stdout=tlf)
+        rval = process.wait()
+        dndf = '%s.dnd' % self.iname
+        if os.path.exists(dndf):
+            tlf.write('\nClustal created the following dnd file for your information:\n')
+            dnds = open('%s.dnd' % self.iname,'r').readlines()
+	    for row in dnds:
+                tlf.write(row)
+            tlf.write('\n')
+        tlf.close()
+        os.unlink(self.iname)
+    
+
+
+if __name__ == "__main__":
+    op = optparse.OptionParser()
+    op.add_option('-i', '--input', default=None)
+    op.add_option('-o', '--output', default=None)
+    op.add_option('-t', '--outname', default="rgClustal")
+    op.add_option('-s', '--out_order', default='ALIGNMENT')
+    op.add_option('-f', '--outform', default='CLUSTAL')
+    op.add_option('-e', '--seq_range_end',default=None)
+    op.add_option('-b', '--seq_range_start',default=None)
+    op.add_option('-l','--outlog',default='rgClustalw.log')
+    op.add_option('-q', '--outseqnos',default=None)    
+    op.add_option('-d', '--dnarna',default='DNA')    
+    
+    opts, args = op.parse_args()
+    assert opts.input <> None
+    assert os.path.isfile(opts.input)
+    c = Clustrunner(opts)
+    c.run()
+    
+            
+