def test_fasta2select_aligned(self):
"""test align.fasta2select() on aligned FASTA (Issue 112)"""
sel = align.fasta2select(self.seq, is_aligned=True)
# length of the output strings, not residues or anything real...
assert len(
sel['reference']) == 30623, "selection string has unexpected length"
assert len(
sel['mobile']) == 30623, "selection string has unexpected length"
def test_fasta2select_aligned(self):
"""test align.fasta2select() on aligned FASTA (Issue 112)"""
from MDAnalysis.analysis.align import fasta2select
sel = fasta2select(self.seq, is_aligned=True)
# length of the output strings, not residues or anything real...
assert_equal(len(sel['reference']), 30623, err_msg="selection string has unexpected length")
assert_equal(len(sel['mobile']), 30623, err_msg="selection string has unexpected length")
def test_fasta2select_aligned(self):
"""test align.fasta2select() on aligned FASTA (Issue 112)"""
sel = align.fasta2select(self.seq, is_aligned=True)
# length of the output strings, not residues or anything real...
assert len(
sel['reference']) == 30623, "selection string has unexpected length"
assert len(
sel['mobile']) == 30623, "selection string has unexpected length"
def test_fasta2select_aligned(self):
"""test align.fasta2select() on aligned FASTA (Issue 112)"""
from MDAnalysis.analysis.align import fasta2select
sel = fasta2select(self.seq, is_aligned=True)
# length of the output strings, not residues or anything real...
assert_equal(len(sel['reference']), 30623, err_msg="selection string has unexpected length")
assert_equal(len(sel['mobile']), 30623, err_msg="selection string has unexpected length")
def test_fasta2select_ClustalW(self):
"""test align.fasta2select() with calling ClustalW (Issue 113)"""
# note: will not be run if clustalw is not installed
from MDAnalysis.analysis.align import fasta2select
sel = fasta2select(self.seq, is_aligned=False, alnfilename=self.alnfile, treefilename=self.treefile)
# numbers computed from alignment with clustalw 2.1 on Mac OS X [orbeckst]
# length of the output strings, not residues or anything real...
assert_equal(len(sel['reference']), 23080, err_msg="selection string has unexpected length")
assert_equal(len(sel['mobile']), 23090, err_msg="selection string has unexpected length")
def test_fasta2select_ClustalW(self):
"""test align.fasta2select() with calling ClustalW (Issue 113)"""
# note: will not be run if clustalw is not installed
from MDAnalysis.analysis.align import fasta2select
sel = fasta2select(self.seq, is_aligned=False, alnfilename=self.alnfile, treefilename=self.treefile)
# numbers computed from alignment with clustalw 2.1 on Mac OS X [orbeckst]
# length of the output strings, not residues or anything real...
assert_equal(len(sel['reference']), 23080, err_msg="selection string has unexpected length")
assert_equal(len(sel['mobile']), 23090, err_msg="selection string has unexpected length")
def test_fasta2select_file(self, tmpdir):
"""test align.fasta2select() on a non-aligned FASTA with default
filenames"""
with tmpdir.as_cwd():
sel = align.fasta2select(self.seq, is_aligned=False,
alnfilename=None, treefilename=None)
assert len(sel['reference']) == 23080, ("selection string has"
"unexpected length")
assert len(sel['mobile']) == 23090, ("selection string has"
"unexpected length")
def test_fasta2select_ClustalW(self):
"""MDAnalysis.analysis.align: test fasta2select() with ClustalW (Issue 113)"""
sel = align.fasta2select(self.seq, is_aligned=False,
alnfilename=self.alnfile,
treefilename=self.treefile)
# numbers computed from alignment with clustalw 2.1 on Mac OS X
# [orbeckst] length of the output strings, not residues or anything
# real...
assert_equal(len(sel['reference']), 23080,
err_msg="selection string has unexpected length")
assert_equal(len(sel['mobile']), 23090,
err_msg="selection string has unexpected length")
def test_fasta2select_ClustalW(self, tmpdir):
"""MDAnalysis.analysis.align: test fasta2select() with ClustalW (Issue 113)"""
alnfile = str(tmpdir.join('alignmentprocessing.aln'))
treefile = str(tmpdir.join('alignmentprocessing.dnd'))
sel = align.fasta2select(self.seq, is_aligned=False,
alnfilename=alnfile, treefilename=treefile)
# numbers computed from alignment with clustalw 2.1 on Mac OS X
# [orbeckst] length of the output strings, not residues or anything
# real...
assert len(
sel['reference']) == 23080, "selection string has unexpected length"
assert len(
sel['mobile']) == 23090, "selection string has unexpected length"
def test_fasta2select_ClustalW(self, tmpdir):
"""MDAnalysis.analysis.align: test fasta2select() with ClustalW (Issue 113)"""
alnfile = str(tmpdir.join('alignmentprocessing.aln'))
treefile = str(tmpdir.join('alignmentprocessing.dnd'))
sel = align.fasta2select(self.seq, is_aligned=False,
alnfilename=alnfile, treefilename=treefile)
# numbers computed from alignment with clustalw 2.1 on Mac OS X
# [orbeckst] length of the output strings, not residues or anything
# real...
assert len(
sel['reference']) == 23080, "selection string has unexpected length"
assert len(
sel['mobile']) == 23090, "selection string has unexpected length"
def test_fasta2select_ClustalW(self):
"""MDAnalysis.analysis.align: test fasta2select() with ClustalW (Issue 113)"""
sel = align.fasta2select(self.seq,
is_aligned=False,
alnfilename=self.alnfile,
treefilename=self.treefile)
# numbers computed from alignment with clustalw 2.1 on Mac OS X
# [orbeckst] length of the output strings, not residues or anything
# real...
assert_equal(len(sel['reference']),
23080,
err_msg="selection string has unexpected length")
assert_equal(len(sel['mobile']),
23090,
err_msg="selection string has unexpected length")
