Mercurial > repos > devteam > clustalw
view rgClustalw.py @ 1:973f9ca114fb draft
planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
author | devteam |
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date | Tue, 21 Jul 2015 14:16:31 -0400 |
parents | 7cc64024fe92 |
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""" 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()