def test_blastp(self):
"""Pairwise BLASTP search."""
global exe_names
cline = Applications.NcbiblastpCommandline(
exe_names["blastp"],
query="Fasta/rose.pro",
subject="GenBank/NC_005816.faa",
evalue=1)
self.assertEqual(str(cline), _escape_filename(exe_names["blastp"]) +
" -query Fasta/rose.pro -evalue 1" +
" -subject GenBank/NC_005816.faa")
child = subprocess.Popen(str(cline),
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
universal_newlines=True,
shell=(sys.platform != "win32"))
stdoutdata, stderrdata = child.communicate()
return_code = child.returncode
self.assertEqual(return_code, 0, "Got error code %i back from:\n%s"
% (return_code, cline))
# Used to get 10 matches from 10 pairwise searches,
# as of NCBI BLAST+ 2.3.0 only get 1 Query= line:
if stdoutdata.count("Query= ") == 10:
if stdoutdata.count("***** No hits found *****") == 7:
# This happens with BLAST 2.2.26+ which is potentially a bug
pass
else:
self.assertEqual(9, stdoutdata.count("***** No hits found *****"))
else:
# Assume this is NCBI BLAST+ 2.3.0 or later,
self.assertEqual(1, stdoutdata.count("Query= "))
self.assertEqual(0, stdoutdata.count("***** No hits found *****"))
def test_tblastn(self):
"""Pairwise TBLASTN search"""
global exe_names
cline = Applications.NcbitblastnCommandline(
exe_names["tblastn"],
query="GenBank/NC_005816.faa",
subject="GenBank/NC_005816.fna",
evalue="1e-6")
self.assertEqual(
str(cline),
_escape_filename(exe_names["tblastn"]) +
" -query GenBank/NC_005816.faa -evalue 1e-6" +
" -subject GenBank/NC_005816.fna")
child = subprocess.Popen(str(cline),
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
universal_newlines=True,
shell=(sys.platform != "win32"))
stdoutdata, stderrdata = child.communicate()
return_code = child.returncode
self.assertEqual(
return_code, 0,
"Got error code %i back from:\n%s" % (return_code, cline))
self.assertEqual(10, stdoutdata.count("Query= "))
self.assertEqual(0, stdoutdata.count("***** No hits found *****"))
def test_fasta_db_nucl(self):
"""Test makeblastdb wrapper with nucleotide database."""
global exe_names
cline = Applications.NcbimakeblastdbCommandline(
exe_names["makeblastdb"],
input_file="GenBank/NC_005816.fna",
dbtype="nucl",
hash_index=True,
max_file_sz="20MB",
parse_seqids=True,
taxid=10)
self.assertEqual(str(cline),
_escape_filename(exe_names["makeblastdb"]) +
" -dbtype nucl -in GenBank/NC_005816.fna"
" -parse_seqids -hash_index -max_file_sz 20MB"
" -taxid 10")
child = subprocess.Popen(str(cline),
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
universal_newlines=True,
shell=(sys.platform != "win32"))
stdoutdata, stderrdata = child.communicate()
return_code = child.returncode
self.assertTrue(os.path.isfile("GenBank/NC_005816.fna.nhd"))
self.assertTrue(os.path.isfile("GenBank/NC_005816.fna.nhi"))
self.assertTrue(os.path.isfile("GenBank/NC_005816.fna.nhr"))
self.assertTrue(os.path.isfile("GenBank/NC_005816.fna.nin"))
self.assertTrue(os.path.isfile("GenBank/NC_005816.fna.nog"))
self.assertTrue(os.path.isfile("GenBank/NC_005816.fna.nsd"))
self.assertTrue(os.path.isfile("GenBank/NC_005816.fna.nsi"))
self.assertTrue(os.path.isfile("GenBank/NC_005816.fna.nsq"))
def test_requires_dbtype(self):
"""Check that dbtype throws error if not set."""
global exe_names
cline = Applications.NcbimakeblastdbCommandline(
exe_names["makeblastdb"], input_file="GenBank/NC_005816.faa")
with self.assertRaises(ValueError):
str(cline)
def test_blastp(self):
"""Pairwise BLASTP search"""
global exe_names
cline = Applications.NcbiblastpCommandline(
exe_names["blastp"],
query="Fasta/rose.pro",
subject="GenBank/NC_005816.faa",
evalue=1)
self.assertEqual(str(cline), exe_names["blastp"] \
+ " -query Fasta/rose.pro -evalue 1" \
+ " -subject GenBank/NC_005816.faa")
child = subprocess.Popen(str(cline),
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
universal_newlines=True,
shell=(sys.platform != "win32"))
stdoutdata, stderrdata = child.communicate()
return_code = child.returncode
self.assertEqual(
return_code, 0,
"Got error code %i back from:\n%s" % (return_code, cline))
self.assertEqual(10, stdoutdata.count("Query= "))
if stdoutdata.count("***** No hits found *****") == 7:
#This happens with BLAST 2.2.26+ which is potentially a bug
pass
else:
self.assertEqual(9, stdoutdata.count("***** No hits found *****"))
def test_fasta_db_prot_legacy(self):
"""Test makeblastdb wrapper with protein database legacy, version 4."""
global exe_names
cline = Applications.NcbimakeblastdbCommandline(
exe_names["makeblastdb"],
blastdb_version=4,
input_file="GenBank/NC_005816.faa",
dbtype="prot",
hash_index=True,
max_file_sz="20MB",
parse_seqids=True,
taxid=10,
)
self.assertEqual(
str(cline),
_escape_filename(exe_names["makeblastdb"]) + " -blastdb_version 4"
" -dbtype prot -in GenBank/NC_005816.faa"
" -parse_seqids -hash_index -max_file_sz 20MB"
" -taxid 10",
)
child = subprocess.Popen(
str(cline),
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
universal_newlines=True,
shell=(sys.platform != "win32"),
)
stdoutdata, stderrdata = child.communicate()
return_code = child.returncode
self.assertTrue(os.path.isfile("GenBank/NC_005816.faa.phd"))
self.assertTrue(os.path.isfile("GenBank/NC_005816.faa.phi"))
self.assertTrue(os.path.isfile("GenBank/NC_005816.faa.phr"))
self.assertTrue(os.path.isfile("GenBank/NC_005816.faa.pin"))
self.assertTrue(os.path.isfile("GenBank/NC_005816.faa.pog"))
self.assertTrue(
os.path.isfile("GenBank/NC_005816.faa.psd")
or os.path.isfile("GenBank/NC_005816.faa.pnd")
)
self.assertTrue(
os.path.isfile("GenBank/NC_005816.faa.psi")
or os.path.isfile("GenBank/NC_005816.faa.pni")
)
self.assertTrue(os.path.isfile("GenBank/NC_005816.faa.psq"))
def _get_alignments(seq_u, atom_u, seq_b, atom_b):
"""
Get alignment between two chains.
Does structural and sequence alignment.
"""
fasta_u = _tmp_fasta(seq_u)
fasta_b = _tmp_fasta(seq_b)
# Only use small word size for small sequences.
# TODO. This is a bit brittle.
word_size = 2 if len(seq_u) < 10 and len(seq_b) < 10 else 3
blastp_cline = app.NcbiblastpCommandline(
subject=fasta_u, query=fasta_b,
outfmt="'10 qstart qend sstart send qseq sseq ppos evalue'",
num_alignments=1, word_size=word_size, culling_limit=1, evalue=0.1)
out, err = blastp_cline()
# The trailing token is empty.
alignments = [x for x in out.split('\n') if x]
b2r, u2r = {}, {}
b2u, u2b = {}, {}
aligned_pos_b, aligned_pos_u = [], []
all_ppos = []
if len(out) == 0:
# No hits found.
return 0.0, float('inf'), (None, None)
warned = False
if len(alignments) > 1:
logging.warning("More than one alignment found.")
for i, curr in enumerate(alignments):
start_b, end_b, start_u, end_u, align_b, align_u, ppos, evalue = \
curr.split(',')
start_b, end_b = int(start_b), int(end_b)
start_u, end_u = int(start_u), int(end_u)
# logging.info('Alignment {:} (score {:}) from {:} to {:} on bound, '
# '{:} to {:} on unbound.'.format(
# i, evalue, start_b, end_b, start_u, end_u))
idx_b, idx_u = start_b - 1, start_u - 1
assert len(align_u) == len(align_b)
align_size = len(align_u)
for k in range(align_size):
if align_b[k] != '-' and align_u[k] != '-':
if idx_b not in b2u and idx_u not in u2b:
b2u[idx_b] = idx_u
u2b[idx_u] = idx_b
aligned_pos_b.append(idx_b)
aligned_pos_u.append(idx_u)
else:
if not warned:
logging.warning('ignoring double prediction {:} bound '
'to {:} unbound'.format(idx_u, idx_b))
logging.warning('not showing future warnings for this '
'alignment')
warned = True
if align_u[k] != '-':
idx_u += 1
if align_b[k] != '-':
idx_b += 1
all_ppos.append((align_size, float(ppos)))
idx_u, idx_b = 0, 0
idx_r = 1
u2r, b2r = {}, {}
while idx_u != len(seq_u) or idx_b != len(seq_b):
if idx_u in u2b and idx_b in b2u:
u2r[idx_u] = idx_r
b2r[idx_b] = idx_r
idx_u += 1
idx_b += 1
elif idx_u not in u2b and idx_u != len(seq_u):
u2r[idx_u] = idx_r
idx_u += 1
elif idx_b not in b2u and idx_b != len(seq_b):
b2r[idx_b] = idx_r
idx_b += 1
idx_r += 1
total = 0
total_ppos = 0
for align_size, ppos in all_ppos:
total_ppos += ppos * align_size
total += align_size
total_ppos /= total
sup = svd.SVDSuperimposer()
sup.set(atom_u[aligned_pos_u], atom_b[aligned_pos_b])
return total_ppos, sup.get_init_rms(), (b2r, u2r)