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 summary(results):
from settings import get_file
from settings import get_setting
data = get_setting('SUMMARY')
file_path = get_file('SUMMARY_FILE')
pipeline = get_setting('PIPELINE')
with open(file_path,'w') as f:
for number, key in data:
f.write('\n==== step %d - %s (module %s) ====\n' % (number, key, pipeline[number][0]))
f.write(format(results[number][key]))
def __init__(self, icm_file=None, sequence=None, extra=None, *args, **kwargs):
super(Glimmer, self).__init__(*args, **kwargs)
if sequence is None:
sequence = inout.SingleSequenceFileInput().read()
if icm_file is None:
icm_file = get_file("ICM_FILE")
if extra is None:
extra = []
self.sequence = sequence
self.icm_file = icm_file
self.extra = list(extra)
def __init__(self, sequence=None, program="blastn", database="nr", queryextra={}, *args, **kwargs):
super(BlastSearch, self).__init__(*args, **kwargs)
if sequence is None:
with open(get_file("INPUT_FILE")) as f:
sequence = f.read()
if isinstance(sequence, SeqRecord):
sequence = sequence.seq
if not isinstance(sequence, (Seq, basestring)):
sequence = inout.StringOutput().write(sequence)
self.sequence = sequence
self.program = program
self.database = database
self.queryextra = queryextra
def __init__(self, file=None, *args, **kwargs):
super(FileInputOutput, self).__init__(*args, **kwargs)
if file is None:
from settings import get_file
file = get_file(self.default_file)
self.file = file
def run(self):
Bio.Phylo.draw_graphviz(self.tree)
pylab.savefig(get_file('TREE_IMAGE'))
return {}