def run(self):
exe = get_setting('CLUSTALW_PATH')
tree_file = get_file('CLUSTALW_NEWTREE', None)
if tree_file is None:
tree_file = create_tmp()
cline = ClustalwCommandline(exe, infile=self.input, newtree=tree_file)
build_tree_out, build_tree_err = cline()
result = {
'tree': Bio.Phylo.read(tree_file, 'newick'),
'tree_out': build_tree_out,
'tree_err': build_tree_err,
}
if self.only_tree:
return result
outfile = get_file('CLUSTALW_OUTFILE', None)
if outfile is None:
outfile = create_tmp()
cline = ClustalwCommandline(exe, infile=self.input, outfile=outfile)
###Fix "p.checker_function = lambda x: os.path.exists"
param = [i for i,p in enumerate(cline.parameters)
if 'usetree' in p.names]
cline.parameters[param[0]].checker_function = os.path.exists
###
setattr(cline, 'usetree', tree_file)
align_out, align_err = cline()
result.update({
'align_out': align_out,
'align_err': align_err,
'alignment': inout.AlignFileInput(file=outfile, format='clustal').read(),
})
return result
def run_glimmer(self):
input_file = create_tmp()
inout.FileOutput(input_file).write(self.sequence)
output_file = get_file("GLIMMER_OUTPUT", None)
if output_file is None:
output_file = create_tmp()
exit_code = subprocess.call([get_file("GLIMMER_PATH"), input_file, self.icm_file, output_file] + self.extra)
return exit_code, output_file
def __init__(self, input=None, sequences=None, only_tree=False, *args, **kwargs):
super(Alignment, self).__init__(*args, **kwargs)
from settings import get_setting
if sequences is not None:
input = create_tmp()
inout.FileOutput(input).write(sequences)
if input is None:
self.input = get_setting('INPUT_FILE')
else:
self.input = input
self.only_tree = only_tree
