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1 """
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2 rgclustalw.py
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3 wrapper for clustalw necessitated by bad choice of output path for .dnd file based on input file. Naughty.
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4 Copyright ross lazarus march 2011
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5 All rights reserved
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6 Licensed under the LGPL
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7 """
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8
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9 import sys,optparse,os,subprocess,tempfile,shutil
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10
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11 class Clustrunner:
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12 """
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13 """
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14 def __init__(self,opts=None):
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15 self.opts = opts
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16 self.iname = 'infile_copy'
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17 shutil.copy(self.opts.input,self.iname)
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18
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19 def run(self):
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20 tlf = open(self.opts.outlog,'w')
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21 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)]
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22 if self.opts.seq_range_end <> None and self.opts.seq_range_start <> None:
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23 cl.append('-RANGE=%s,%s' % (self.opts.seq_range_start,self.opts.seq_range_end))
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24 if self.opts.outform=='CLUSTAL' and self.opts.outseqnos <> None:
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25 cl.append('-SEQNOS=ON')
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26 process = subprocess.Popen(' '.join(cl), shell=True, stderr=tlf, stdout=tlf)
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27 rval = process.wait()
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28 dndf = '%s.dnd' % self.iname
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29 if os.path.exists(dndf):
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30 tlf.write('\nClustal created the following dnd file for your information:\n')
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31 dnds = open('%s.dnd' % self.iname,'r').readlines()
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32 for row in dnds:
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33 tlf.write(row)
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34 tlf.write('\n')
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35 tlf.close()
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36 os.unlink(self.iname)
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37
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38
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39
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40 if __name__ == "__main__":
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41 op = optparse.OptionParser()
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42 op.add_option('-i', '--input', default=None)
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43 op.add_option('-o', '--output', default=None)
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44 op.add_option('-t', '--outname', default="rgClustal")
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45 op.add_option('-s', '--out_order', default='ALIGNMENT')
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46 op.add_option('-f', '--outform', default='CLUSTAL')
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47 op.add_option('-e', '--seq_range_end',default=None)
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48 op.add_option('-b', '--seq_range_start',default=None)
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49 op.add_option('-l','--outlog',default='rgClustalw.log')
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50 op.add_option('-q', '--outseqnos',default=None)
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51 op.add_option('-d', '--dnarna',default='DNA')
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52
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53 opts, args = op.parse_args()
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54 assert opts.input <> None
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55 assert os.path.isfile(opts.input)
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56 c = Clustrunner(opts)
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57 c.run()
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58
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59
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60
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