def _makeblastdb_plus(seq_fpath, dbtype, outputdb=None):
'It creates the blast db database'
cmd = [get_binary_path('makeblastdb'), '-in', seq_fpath, '-dbtype', dbtype]
if outputdb is not None:
cmd.extend(['-out', outputdb])
process = popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
check_process_finishes(process, binary=cmd[0])
def _makeblastdb_plus(seq_fpath, dbtype, outputdb=None):
"It creates the blast db database"
cmd = [get_binary_path("makeblastdb"), "-in", seq_fpath, "-dbtype", dbtype]
if outputdb is not None:
cmd.extend(["-out", outputdb])
process = popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
check_process_finishes(process, binary=cmd[0])
def _makeblastdb_plus(seq_fpath, dbtype, outputdb=None):
'It creates the blast db database'
cmd = [get_binary_path('makeblastdb'), '-in', seq_fpath, '-dbtype', dbtype]
if outputdb is not None:
cmd.extend(['-out', outputdb])
process = popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
check_process_finishes(process, binary=cmd[0])
def _create_bwa_index(index_fpath):
binary = get_binary_path('bwa')
# how many sequences do we have?
n_seqs = [l for l in open(index_fpath) if l[0] == '>']
algorithm = 'bwtsw' if n_seqs > 10000 else 'is'
cmd = [binary, 'index', '-a', algorithm, index_fpath]
process = popen(cmd, stdout=PIPE, stderr=PIPE)
check_process_finishes(process, binary=cmd[0])
def test_check_process(self):
'It checks that a process finishes OK'
binary = 'ls'
process = Popen([binary, '/directorio_que_no_existe'], stderr=PIPE)
try:
check_process_finishes(process, binary)
self.fail('ExternalBinaryErrorExpected')
except ExternalBinaryError, error:
assert binary in str(error)
def test_check_process(self):
"It checks that a process finishes OK"
binary = "ls"
process = Popen([binary, "/directorio_que_no_existe"], stderr=PIPE)
try:
check_process_finishes(process, binary)
self.fail("ExternalBinaryErrorExpected")
except ExternalBinaryError, error:
assert binary in str(error)
def test_check_process(self):
'It checks that a process finishes OK'
binary = 'ls'
process = Popen([binary, '/directorio_que_no_existe'], stderr=PIPE)
try:
check_process_finishes(process, binary)
self.fail('ExternalBinaryErrorExpected')
except ExternalBinaryError, error:
assert binary in str(error)
def _run_estscan(seqs, pep_out_fpath, dna_out_fpath, matrix_fpath):
'It runs estscan in the input seqs'
seq_fhand = write_seqs(seqs, file_format='fasta')
seq_fhand.flush()
binary = get_binary_path('estscan')
cmd = [binary, '-t', pep_out_fpath, '-o', dna_out_fpath, '-M',
matrix_fpath, seq_fhand.name]
process = popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
check_process_finishes(process, binary=cmd[0])
seq_fhand.close()
def _run_estscan(seqs, pep_out_fpath, dna_out_fpath, matrix_fpath):
'It runs estscan in the input seqs'
seq_fhand = write_seqs(seqs, file_format='fasta')
seq_fhand.flush()
binary = get_binary_path('estscan')
cmd = [binary, '-t', pep_out_fpath, '-o', dna_out_fpath, '-M',
matrix_fpath, seq_fhand.name]
process = popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
check_process_finishes(process, binary=cmd[0])
seq_fhand.close()
def get_or_create_bowtie2_index(fpath, directory=None):
"it creates the bowtie2 index"
binary = get_binary_path('bowtie2-build')
if directory is not None:
index_fpath = os.path.join(directory, os.path.basename(fpath))
else:
index_fpath = fpath
if not _bowtie2_index_exists(index_fpath):
cmd = [binary, '-f', fpath, index_fpath]
process = popen(cmd, stdout=PIPE, stderr=PIPE)
check_process_finishes(process, binary=cmd[0])
return index_fpath
def do_blast(query_fpath, db_fpath, program, out_fpath, params=None):
"It does a blast"
if not params:
params = {}
evalue = params.get("evalue", 0.001)
task = params.get("task", "megablast")
outfmt = str(params.get("outfmt", 5))
assert task in ("blastn", "blastn-short", "dc-megablast", "megablast", "rmblastn")
if program not in ("blastn", "blastp", "blastx", "tblastx", "tblastn"):
raise ValueError("The given program is invalid: " + str(program))
binary = get_binary_path(program)
cmd = [binary, "-query", query_fpath, "-db", db_fpath, "-out", out_fpath]
cmd.extend(["-evalue", str(evalue), "-task", task])
cmd.extend(["-outfmt", outfmt])
process = popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
check_process_finishes(process, binary=cmd[0])
def _do_blast_local(query_fpath, db_fpath, program, out_fpath, params=None):
"It does a blast"
if not params:
params = {}
evalue, task = _parse_blast_params(params, program)
if "outfmt" in params:
outfmt = params["outfmt"]
del params["outfmt"]
else:
outfmt = 5
if program not in ("blastn", "blastp", "blastx", "tblastx", "tblastn"):
raise ValueError("The given program is invalid: " + str(program))
binary = get_binary_path(program)
cmd = [binary, "-query", query_fpath, "-db", db_fpath, "-out", out_fpath]
cmd.extend(["-evalue", str(evalue), "-outfmt", str(outfmt)])
if task:
cmd.extend(["-task", task])
if params:
for key, value in params.viewitems():
cmd.extend(("-" + key, str(value)))
process = popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
check_process_finishes(process, binary=cmd[0])
def _do_blast_local(query_fpath, db_fpath, program, out_fpath, params=None):
'It does a blast'
if not params:
params = {}
evalue, task = _parse_blast_params(params, program)
if 'outfmt' in params:
outfmt = params['outfmt']
del params['outfmt']
else:
outfmt = 5
if program not in ('blastn', 'blastp', 'blastx', 'tblastx', 'tblastn'):
raise ValueError('The given program is invalid: ' + str(program))
binary = get_binary_path(program)
cmd = [binary, '-query', query_fpath, '-db', db_fpath, '-out', out_fpath]
cmd.extend(['-evalue', str(evalue), '-outfmt', str(outfmt)])
if task:
cmd.extend(['-task', task])
if params:
for key, value in params.viewitems():
cmd.extend(('-' + key, str(value)))
process = popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
check_process_finishes(process, binary=cmd[0])
def _do_blast_local(query_fpath, db_fpath, program, out_fpath, params=None):
'It does a blast'
if not params:
params = {}
evalue, task = _parse_blast_params(params, program)
if 'outfmt' in params:
outfmt = params['outfmt']
del params['outfmt']
else:
outfmt = 5
if program not in ('blastn', 'blastp', 'blastx', 'tblastx', 'tblastn'):
raise ValueError('The given program is invalid: ' + str(program))
binary = get_binary_path(program)
cmd = [binary, '-query', query_fpath, '-db', db_fpath, '-out', out_fpath]
cmd.extend(['-evalue', str(evalue), '-outfmt', str(outfmt)])
if task:
cmd.extend(['-task', task])
if params:
for key, value in params.viewitems():
cmd.extend(('-' + key, str(value)))
process = popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
check_process_finishes(process, binary=cmd[0])
class UtilsTest(unittest.TestCase):
'It tests the miscelaneous utilities.'
def test_rel_symlink(self):
'It tests various cases of rel symlinks'
tempdir = TemporaryDir()
try:
hola = os.path.join(tempdir.name, 'hola')
os.mkdir(hola)
caracola = os.path.join(tempdir.name, 'caracola')
rel_symlink(hola, caracola)
assert os.path.exists(caracola)
fname = os.path.join(hola, 'fname')
open(fname, 'w')
caracola2 = os.path.join(tempdir.name, 'caracola2')
rel_symlink(fname, caracola2)
assert os.path.exists(caracola2)
path2 = os.path.join(tempdir.name, 'dir1', 'dir2')
os.makedirs(path2)
caracola3 = os.path.join(path2, 'caracola3')
rel_symlink(hola, caracola3)
assert os.path.exists(caracola3)
finally:
tempdir.close()
def test_check_process(self):
'It checks that a process finishes OK'
binary = 'ls'
process = Popen([binary, '/directorio_que_no_existe'], stderr=PIPE)
try:
check_process_finishes(process, binary)
self.fail('ExternalBinaryErrorExpected')
except ExternalBinaryError, error:
assert binary in str(error)
stderr = NamedTemporaryFile()
process = Popen([binary, '/directorio_que_no_existe'], stderr=stderr)
try:
check_process_finishes(process, binary, stderr=stderr)
except ExternalBinaryError, error:
assert binary in str(error)
try:
check_process_finishes(process, binary)
self.fail('ExternalBinaryErrorExpected')
except ExternalBinaryError, error:
assert binary in str(error)
stderr = NamedTemporaryFile()
process = Popen([binary, '/directorio_que_no_existe'], stderr=stderr)
try:
check_process_finishes(process, binary, stderr=stderr)
except ExternalBinaryError, error:
assert binary in str(error)
cmd = [binary]
process = Popen(cmd, stdout=PIPE)
check_process_finishes(process, binary)
def test_popen(self):
'It checks that we can create a process'
try:
popen(['bad_binary'])
self.fail()
except MissingBinaryError:
pass
popen(['ls'], stdout=PIPE)
def test_io_open(self):
'It checks the file wrapping in ReaderBuffers'
try:
check_process_finishes(process, binary)
self.fail('ExternalBinaryErrorExpected')
except ExternalBinaryError, error:
assert binary in str(error)
stderr = NamedTemporaryFile()
process = Popen([binary, '/directorio_que_no_existe'], stderr=stderr)
try:
check_process_finishes(process, binary, stderr=stderr)
except ExternalBinaryError, error:
assert binary in str(error)
cmd = [binary]
process = Popen(cmd, stdout=PIPE)
check_process_finishes(process, binary)
def test_popen(self):
'It checks that we can create a process'
try:
popen(['bad_binary'])
self.fail()
except MissingBinaryError:
pass
popen(['ls'], stdout=PIPE)
def test_io_open(self):
'It checks the file wrapping in ReaderBuffers'
