def test_properties(self):
"""Test passing options via properties."""
cline = ClustalwCommandline(clustalw_exe)
cline.infile = "Fasta/f002"
cline.outfile = "temp_test.aln"
cline.align = True
self.standard_test_procedure(cline)
def test_properties(self):
"""Test passing options via properties."""
cline = ClustalwCommandline(clustalw_exe)
cline.infile = "Fasta/f002"
cline.outfile = "temp_test.aln"
cline.align = True
self.standard_test_procedure(cline)
# -*- coding: utf-8 -*-
"""
Created on Wed Dec 21 22:34:11 2016
@author: sbassi
"""
import os
from Bio.Align.Applications import ClustalwCommandline
base_dir = os.getcwd()
clustalw_exe = os.path.join(base_dir, 'clustalw2')
#cl = MultipleAlignCL('conglycinin.fasta')
data = os.path.join('samples','conglycinin.fasta')
cl = ClustalwCommandline(clustalw_exe, infile=data)
cl.outfile = 'cltest.aln'
print('Command line: {}'.format(cl))
cl()
# -*- coding: utf-8 -*-
"""
Created on Wed Dec 21 22:34:11 2016
@author: sbassi
"""
import os
from Bio.Align.Applications import ClustalwCommandline
base_dir = os.getcwd()
clustalw_exe = os.path.join(base_dir, 'clustalw2')
#cl = MultipleAlignCL('conglycinin.fasta')
data = os.path.join('samples', 'conglycinin.fasta')
cl = ClustalwCommandline(clustalw_exe, infile=data)
cl.outfile = 'cltest.aln'
print('Command line: {}'.format(cl))
cl()
