def qiime_blast_seqs(seqs,
blast_constructor=Blastall,
blast_program='blastn',
blast_db=None,
refseqs=None,
refseqs_fp=None,
blast_mat_root=None,
params={},
WorkingDir=None,
seqs_per_blast_run=1000,
HALT_EXEC=False):
"""Blast list of sequences.
seqs: a list (or object with list-like interace) of (seq_id, seq)
tuples (e.g., the output of MinimalFastaParser)
"""
assert blast_db or refseqs_fp or refseqs, \
'Must provide either a blast_db or a fasta '+\
'filepath containing sequences to build one.'
if refseqs_fp:
blast_db, db_files_to_remove =\
build_blast_db_from_fasta_path(refseqs_fp,output_dir=WorkingDir)
elif refseqs:
blast_db, db_files_to_remove =\
build_blast_db_from_fasta_file(refseqs,output_dir=WorkingDir)
else:
db_files_to_remove = []
params["-d"] = blast_db
params["-p"] = blast_program
blast_app = blast_constructor(params=params,
blast_mat_root=blast_mat_root,
InputHandler='_input_as_seq_id_seq_pairs',
WorkingDir=WorkingDir,
SuppressStderr=True,
HALT_EXEC=HALT_EXEC)
current_seqs = []
blast_results = BlastResult([])
for seq in seqs:
current_seqs.append(seq)
if len(current_seqs) % seqs_per_blast_run == 0:
if blast_results:
blast_results.update(\
BlastResult(blast_app(current_seqs)['StdOut']))
else:
blast_results = BlastResult(blast_app(current_seqs)['StdOut'])
current_seqs = []
# clean-up run: blast the remaining sequences
blast_results.update(\
BlastResult(blast_app(current_seqs)['StdOut']))
remove_files(db_files_to_remove)
return blast_results
def setUp(self):
"""
"""
self.refseqs1 = refseqs1.split('\n')
self.inseqs1 = inseqs1.split('\n')
self.blast_db, db_files_to_remove =\
build_blast_db_from_fasta_file(self.refseqs1,output_dir='/tmp/')
self.files_to_remove = db_files_to_remove
self.refseqs1_fp = get_tmp_filename(\
tmp_dir='/tmp/', prefix="BLAST_temp_db_", suffix=".fasta")
fasta_f = open(self.refseqs1_fp, 'w')
fasta_f.write(refseqs1)
fasta_f.close()
self.files_to_remove = db_files_to_remove + [self.refseqs1_fp]
def setUp(self):
"""
"""
self.refseqs1 = refseqs1.split('\n')
self.inseqs1 = inseqs1.split('\n')
self.blast_db, db_files_to_remove =\
build_blast_db_from_fasta_file(self.refseqs1,output_dir='/tmp/')
self.files_to_remove = db_files_to_remove
self.refseqs1_fp = get_tmp_filename(\
tmp_dir='/tmp/', prefix="BLAST_temp_db_", suffix=".fasta")
fasta_f = open(self.refseqs1_fp,'w')
fasta_f.write(refseqs1)
fasta_f.close()
self.files_to_remove = db_files_to_remove + [self.refseqs1_fp]
def test_build_blast_db_from_fasta_file(self):
"""build_blast_db_from_fasta_file works with open files as input
"""
blast_db, db_files = build_blast_db_from_fasta_file(open(self.in_aln1_fp), output_dir="/tmp/")
self.assertTrue(blast_db.startswith("/tmp/BLAST_temp_db"))
self.assertTrue(blast_db.endswith(".fasta"))
expected_db_files = set(
[blast_db] + [blast_db + ext for ext in [".nhr", ".nin", ".nsq", ".nsd", ".nsi", ".log"]]
)
self.assertEqual(set(db_files), expected_db_files)
# result returned when blasting against new db
self.assertEqual(len(blastn(self.test_seq, blast_db=blast_db, e_value=0.0)), 1)
# Make sure all db_files exist
for fp in db_files:
self.assertTrue(exists(fp))
# Remove all db_files exist
remove_files(db_files)
# Make sure nothing weird happened in the remove
for fp in db_files:
self.assertFalse(exists(fp))
def test_build_blast_db_from_fasta_file(self):
"""build_blast_db_from_fasta_file works with open files as input
"""
blast_db, db_files = \
build_blast_db_from_fasta_file(open(self.in_aln1_fp),output_dir='/tmp/')
self.assertTrue(blast_db.startswith('/tmp/BLAST_temp_db'))
self.assertTrue(blast_db.endswith('.fasta'))
expected_db_files = set([blast_db] + [blast_db + ext\
for ext in ['.nhr','.nin','.nsq','.nsd','.nsi','.log']])
self.assertEqual(set(db_files), expected_db_files)
# result returned when blasting against new db
self.assertEqual(\
len(blastn(self.test_seq,blast_db=blast_db,e_value=0.0)),1)
# Make sure all db_files exist
for fp in db_files:
self.assertTrue(exists(fp))
# Remove all db_files exist
remove_files(db_files)
# Make sure nothing weird happened in the remove
for fp in db_files:
self.assertFalse(exists(fp))
