def xtest_remote_blast(self):
'It does a remote blast search'
seq_fhand = NamedTemporaryFile()
fasta = '>seq1\nCTAGTCTAGTCGTAGTCATGGCTGTAGTCTAGTCTACGATTCGTATCAGTTGT'
fasta += 'GTGACATCGATCATGTTGTATTGTGTACTATACACACACGTAGGTCGACTATCGTAGC\n'
seq_fhand.write(fasta)
seq_fhand.flush()
out_fhand = NamedTemporaryFile()
do_blast(seq_fhand.name,
'nt',
program='blastn',
out_fpath=out_fhand.name,
remote=True)
assert '</BlastOutput>' in open(out_fhand.name).read()
# fail if outfmt is not xml
try:
params = {'outfmt': 'txt'}
do_blast(seq_fhand.name,
'nt',
program='blastn',
out_fpath=out_fhand.name,
remote=True,
params=params)
self.fail()
except RuntimeError:
pass
def test_blast_search(self):
'It does a blast search'
db_name = 'arabidopsis_genes'
seq_fpath = os.path.join(TEST_DATA_DIR, db_name)
db_dir = TemporaryDir(prefix='blast_dbs_')
try:
db_fpath = get_or_create_blastdb(seq_fpath, directory=db_dir.name,
dbtype='nucl')
query_fhand = NamedTemporaryFile()
query_fhand.write(open(seq_fpath).read(200))
query_fhand.flush()
out_fhand = NamedTemporaryFile()
do_blast(seq_fpath, db_fpath, program='blastn',
out_fpath=out_fhand.name)
assert '</BlastOutput>' in open(out_fhand.name).read()
finally:
db_dir.close()
def test_remote_blast(self):
'It does a remote blast search'
seq_fhand = NamedTemporaryFile()
fasta = '>seq1\nCTAGTCTAGTCGTAGTCATGGCTGTAGTCTAGTCTACGATTCGTATCAGTTGT'
fasta += 'GTGACATCGATCATGTTGTATTGTGTACTATACACACACGTAGGTCGACTATCGTAGC\n'
seq_fhand.write(fasta)
seq_fhand.flush()
out_fhand = NamedTemporaryFile()
do_blast(seq_fhand.name, 'nt', program='blastn',
out_fpath=out_fhand.name, remote=True)
assert '</BlastOutput>' in open(out_fhand.name).read()
# fail if outfmt is not xml
try:
do_blast(seq_fhand.name, 'nt', program='blastn',
out_fpath=out_fhand.name, remote=True, params={'outfmt':'txt'})
self.fail()
except RuntimeError:
pass
def test_blast_search(self):
'It does a blast search'
db_name = 'arabidopsis_genes'
seq_fpath = os.path.join(TEST_DATA_DIR, db_name)
db_dir = TemporaryDir(prefix='blast_dbs_')
try:
db_fpath = get_or_create_blastdb(seq_fpath,
directory=db_dir.name,
dbtype='nucl')
query_fhand = NamedTemporaryFile()
query_fhand.write(open(seq_fpath).read(200))
query_fhand.flush()
out_fhand = NamedTemporaryFile()
do_blast(seq_fpath,
db_fpath,
program='blastn',
out_fpath=out_fhand.name)
assert '</BlastOutput>' in open(out_fhand.name).read()
finally:
db_dir.close()