view rgClustalw.py @ 2:f8aad74cc8c1 draft

planemo upload commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d

"""
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()