def test_as_refpkg(self):
with wrap.as_refpkg(self.sequences) as refpkg:
self.assertTrue(os.path.isdir(refpkg.path))
if which('rppr'):
out = subprocess.check_output(['rppr', 'check', '-c', refpkg.path])
self.assertTrue('OK!' in out, out)
class FilterOutliersFunctions(unittest.TestCase):
def setUp(self):
pass
def test_parse_usearch_allpairs(self):
filename = util.data_path('e_faecalis.head.allpairs')
with open(util.data_path('e_faecalis.head.fasta')) as f:
seqs = SeqIO.parse(f, 'fasta')
seqnames = [seq.id for seq in seqs]
distmat = filter_outliers.parse_usearch_allpairs(filename, seqnames)
self.assertEqual(len(seqnames), distmat.shape[0])
@unittest.skipUnless(which(wrap.VSEARCH), "{} not found.".format(wrap.VSEARCH))
def test_distmat_pairwise_vsearch(self):
infile = util.data_path('e_faecalis.head.fasta')
taxa, distmat = filter_outliers.distmat_pairwise(
infile, 'foo', 'vsearch', wrap.VSEARCH)
self.assertEqual(distmat.shape[0], len(taxa))
import os.path
import subprocess
import tempfile
import unittest
from Bio import SeqIO
from deenurp import wrap
from deenurp.test import util
from deenurp.util import which
@unittest.skipUnless(which('cmalign'), "cmalign not found.")
class CmAlignTestCase(unittest.TestCase):
def setUp(self):
self.sequences = list(SeqIO.parse(util.data_path('test_input.fasta'), 'fasta'))
def test_nompi(self):
result = list(wrap.cmalign(self.sequences))
self.assertEqual(len(self.sequences), len(result))
def test_mpi(self):
result = list(wrap.cmalign(self.sequences, mpi_args=['-np', '2']))
self.assertEqual(len(self.sequences), len(result))
class CMTestCase(unittest.TestCase):
def test_find_cm(self):
self.assertTrue(os.path.isfile(wrap.CM))
@unittest.skipUnless(which('FastTree'), "FastTree not found")
class AsRefpkgTestCase(unittest.TestCase):
def setUp(self):
