Mercurial > repos > xuebing > sharplabtool
comparison tools/rgenetics/rgClustalw.py @ 0:9071e359b9a3
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| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:37:19 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:9071e359b9a3 |
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| 1 """ | |
| 2 rgclustalw.py | |
| 3 wrapper for clustalw necessitated by bad choice of output path for .dnd file based on input file. Naughty. | |
| 4 Copyright ross lazarus march 2011 | |
| 5 All rights reserved | |
| 6 Licensed under the LGPL | |
| 7 """ | |
| 8 | |
| 9 import sys,optparse,os,subprocess,tempfile,shutil | |
| 10 | |
| 11 class Clustrunner: | |
| 12 """ | |
| 13 """ | |
| 14 def __init__(self,opts=None): | |
| 15 self.opts = opts | |
| 16 self.iname = 'infile_copy' | |
| 17 shutil.copy(self.opts.input,self.iname) | |
| 18 | |
| 19 def run(self): | |
| 20 tlf = open(self.opts.outlog,'w') | |
| 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)] | |
| 22 if self.opts.seq_range_end <> None and self.opts.seq_range_start <> None: | |
| 23 cl.append('-RANGE=%s,%s' % (self.opts.seq_range_start,self.opts.seq_range_end)) | |
| 24 if self.opts.outform=='CLUSTAL' and self.opts.outseqnos <> None: | |
| 25 cl.append('-SEQNOS=ON') | |
| 26 process = subprocess.Popen(' '.join(cl), shell=True, stderr=tlf, stdout=tlf) | |
| 27 rval = process.wait() | |
| 28 dndf = '%s.dnd' % self.iname | |
| 29 if os.path.exists(dndf): | |
| 30 tlf.write('\nClustal created the following dnd file for your information:\n') | |
| 31 dnds = open('%s.dnd' % self.iname,'r').readlines() | |
| 32 for row in dnds: | |
| 33 tlf.write(row) | |
| 34 tlf.write('\n') | |
| 35 tlf.close() | |
| 36 os.unlink(self.iname) | |
| 37 | |
| 38 | |
| 39 | |
| 40 if __name__ == "__main__": | |
| 41 op = optparse.OptionParser() | |
| 42 op.add_option('-i', '--input', default=None) | |
| 43 op.add_option('-o', '--output', default=None) | |
| 44 op.add_option('-t', '--outname', default="rgClustal") | |
| 45 op.add_option('-s', '--out_order', default='ALIGNMENT') | |
| 46 op.add_option('-f', '--outform', default='CLUSTAL') | |
| 47 op.add_option('-e', '--seq_range_end',default=None) | |
| 48 op.add_option('-b', '--seq_range_start',default=None) | |
| 49 op.add_option('-l','--outlog',default='rgClustalw.log') | |
| 50 op.add_option('-q', '--outseqnos',default=None) | |
| 51 op.add_option('-d', '--dnarna',default='DNA') | |
| 52 | |
| 53 opts, args = op.parse_args() | |
| 54 assert opts.input <> None | |
| 55 assert os.path.isfile(opts.input) | |
| 56 c = Clustrunner(opts) | |
| 57 c.run() | |
| 58 | |
| 59 | |
| 60 |