def _get_blast_hits(self, blast_db, seqs):
""" blast each seq in seqs against blast_db and retain good hits
"""
max_evalue = self.Params["Max E value"]
min_percent_identity = self.Params["Min percent identity"]
seq_ids = [s[0] for s in seqs]
result = {}
blast_result = blast_seqs(
seqs, Blastall, blast_db=blast_db, params={"-p": "blastn", "-n": "T"}, add_seq_names=False
)
if blast_result["StdOut"]:
lines = [x for x in blast_result["StdOut"]]
blast_result = BlastResult(lines)
else:
return {}.fromkeys(seq_ids, [])
for seq_id in seq_ids:
blast_result_id = seq_id.split()[0]
try:
result[seq_id] = [
(e["SUBJECT ID"], float(e["E-VALUE"]))
for e in blast_result[blast_result_id][0]
if (float(e["E-VALUE"]) <= max_evalue and float(e["% IDENTITY"]) >= min_percent_identity)
]
except KeyError:
result[seq_id] = []
return result
def _get_blast_hits(self,blast_db,seqs):
""" blast each seq in seqs against blast_db and retain good hits
"""
max_evalue = self.Params['Max E value']
min_percent_identity = self.Params['Min percent identity']
if min_percent_identity < 1.0:
min_percent_identity *= 100.0
seq_ids = [s[0] for s in seqs]
result = {}
blast_result = blast_seqs(\
seqs,Blastall,blast_db=blast_db,\
params={'-p':'blastn','-n':'T'},\
add_seq_names=False)
if blast_result['StdOut']:
lines = [x for x in blast_result['StdOut']]
blast_result = BlastResult(lines)
else:
return {}.fromkeys(seq_ids,[])
for seq_id in seq_ids:
blast_result_id = seq_id.split()[0]
try:
result[seq_id] = [(e['SUBJECT ID'],float(e['E-VALUE'])) \
for e in blast_result[blast_result_id][0]
if (float(e['E-VALUE']) <= max_evalue and \
float(e['% IDENTITY']) >= min_percent_identity)]
except KeyError:
result[seq_id] = []
return result
def _get_blast_hits(self, blast_db, seqs):
""" blast each seq in seqs against blast_db and retain good hits
"""
max_evalue = self.Params['Max E value']
min_percent_identity = self.Params['Min percent identity']
if min_percent_identity < 1.0:
min_percent_identity *= 100.0
seq_ids = [s[0] for s in seqs]
result = {}
blast_result = blast_seqs(\
seqs,Blastall,blast_db=blast_db,\
params={'-p':'blastn','-n':'T'},\
add_seq_names=False)
if blast_result['StdOut']:
lines = [x for x in blast_result['StdOut']]
blast_result = BlastResult(lines)
else:
return {}.fromkeys(seq_ids, [])
for seq_id in seq_ids:
blast_result_id = seq_id.split()[0]
try:
result[seq_id] = [(e['SUBJECT ID'],float(e['E-VALUE'])) \
for e in blast_result[blast_result_id][0]
if (float(e['E-VALUE']) <= max_evalue and \
float(e['% IDENTITY']) >= min_percent_identity)]
except KeyError:
result[seq_id] = []
return result
def get_blast_hits(seqs,
blast_db,
max_e_value=1e-10,
min_pct_identity=0.75,
min_aligned_percent=0.50):
""" blast each seq in seqs against blast_db and retain good hits
"""
max_evalue = max_e_value
min_percent_identity = min_pct_identity
seq_ids = [s[0] for s in seqs]
result = {}
blast_result = blast_seqs(\
seqs,Blastall,blast_db=blast_db,\
params={'-p':'blastn','-n':'F'},\
add_seq_names=False)
if blast_result['StdOut']:
lines = [x for x in blast_result['StdOut']]
blast_result = BlastResult(lines)
else:
return {}.fromkeys(seq_ids, [])
for seq_id, seq in seqs:
blast_result_id = seq_id.split()[0]
min_alignment_length = len(seq) * min_aligned_percent
result[seq_id] = []
if blast_result_id in blast_result:
for e in blast_result[blast_result_id][0]:
if (float(e['E-VALUE']) <= max_evalue and\
float(e['% IDENTITY']) / 100. >= min_percent_identity and\
int(e['ALIGNMENT LENGTH']) >= min_alignment_length):
result[seq_id].append(e)
return result
def get_blast_hits(seqs, blast_db, max_e_value=1e-10, min_pct_identity=0.75, min_aligned_percent=0.50):
""" blast each seq in seqs against blast_db and retain good hits
"""
max_evalue = max_e_value
min_percent_identity = min_pct_identity
seq_ids = [s[0] for s in seqs]
result = {}
blast_result = blast_seqs(
seqs, Blastall, blast_db=blast_db, params={"-p": "blastn", "-n": "F"}, add_seq_names=False
)
if blast_result["StdOut"]:
lines = [x for x in blast_result["StdOut"]]
blast_result = BlastResult(lines)
else:
return {}.fromkeys(seq_ids, [])
for seq_id, seq in seqs:
blast_result_id = seq_id.split()[0]
min_alignment_length = len(seq) * min_aligned_percent
result[seq_id] = []
if blast_result_id in blast_result:
for e in blast_result[blast_result_id][0]:
if (
float(e["E-VALUE"]) <= max_evalue
and float(e["% IDENTITY"]) / 100.0 >= min_percent_identity
and int(e["ALIGNMENT LENGTH"]) >= min_alignment_length
):
result[seq_id].append(e)
return result
def blast_genome(seqs,
blast_db,
e_value,
max_hits,
word_size,
working_dir,
blast_mat_root,
extra_params=[],
DEBUG=True):
"""Blast sequences against all genes in a genome
seqs -- input sequences as strings
blast_db -- path to blast database
e_value -- e_value (float)
max_hits -- maximum sequences detected by BLAST to show
word_size -- word size for initial BLAST screen.
blast_mat_root -- location of BLAST matrix files
extra_params -- additional paramters to pass to BLAST
DEBUG -- display verbose debugging outout
"""
# set up params to use with blastp or
params = {
# matrix
"-M": "BLOSUM62",
# max procs
"-a": "1",
# expectation
"-e": e_value,
# max seqs to show
"-b": max_hits,
# Word size
"-W": word_size,
# max one line descriptions
"-v": max_hits,
# tabular output
"-m": "9",
# program
"-p": "blastn"
}
params.update(extra_params)
output = blast_seqs(seqs,
Blastall,
blast_db=blast_db,
params=params,
WorkingDir=working_dir,
add_seq_names=False,
blast_mat_root=blast_mat_root)
raw_output = [x for x in output['StdOut']]
return raw_output
def blast_genome(seqs,blast_db,e_value,max_hits, word_size, working_dir,\
blast_mat_root, extra_params=[],DEBUG=True):
"""Blast sequences against all genes in a genome
seqs -- input sequences as strings
blast_db -- path to blast database
e_value -- e_value (float)
max_hits -- maximum sequences detected by BLAST to show
word_size -- word size for initial BLAST screen.
blast_mat_root -- location of BLAST matrix files
extra_params -- additional paramters to pass to BLAST
DEBUG -- display verbose debugging outout
"""
# set up params to use with blastp or
params = {
# matrix
"-M":"BLOSUM62",
# max procs
"-a":"1",
# expectation
"-e":e_value,
# max seqs to show
"-b":max_hits,
# Word size
"-W":word_size,
# max one line descriptions
"-v":max_hits,
#tabular output
"-m":"9",
# program
"-p":"blastn"
}
params.update(extra_params)
output=blast_seqs(seqs,\
Blastall,\
blast_db=blast_db,\
params=params,\
WorkingDir=working_dir,\
add_seq_names=False,\
blast_mat_root=blast_mat_root)
raw_output=[x for x in output['StdOut']]
return raw_output