def test_alt_blast_param(self):
"""qiime_blast_seqs: alt blast params give alt results"""
# Fewer blast hits with stricter e-value
inseqs = MinimalFastaParser(self.inseqs1)
actual = qiime_blast_seqs(inseqs,blast_db=self.blast_db,params={'-e':'1e-4'})
# NOTE: A BUG (?) IN THE BlastResult OR THE PARSER RESULTS IN AN EXTRA
# BLAST RESULT IN THE DICT (actual HERE) WITH KEY ''
self.assertTrue('s2_like_seq' in actual)
self.assertFalse('s100' in actual)
def test_w_refseqs_fp(self):
"""qiime_blast_seqs functions refseqs_fp
"""
inseqs = MinimalFastaParser(self.inseqs1)
actual = qiime_blast_seqs(inseqs, refseqs_fp=self.refseqs1_fp)
self.assertEqual(len(actual), 5)
# couple of sanity checks against command line blast
self.assertEqual(actual['s2_like_seq'][0][0]['SUBJECT ID'], 's2')
self.assertEqual(actual['s105'][0][2]['SUBJECT ID'], 's1')
def test_w_refseqs_fp(self):
"""qiime_blast_seqs functions refseqs_fp
"""
inseqs = MinimalFastaParser(self.inseqs1)
actual = qiime_blast_seqs(inseqs,refseqs_fp=self.refseqs1_fp)
self.assertEqual(len(actual),5)
# couple of sanity checks against command line blast
self.assertEqual(actual['s2_like_seq'][0][0]['SUBJECT ID'],'s2')
self.assertEqual(actual['s105'][0][2]['SUBJECT ID'],'s1')
def test_w_preexising_blastdb(self):
"""qiime_blast_seqs functions with pre-existing blast_db
"""
# pre-existing blast db
inseqs = MinimalFastaParser(self.inseqs1)
actual = qiime_blast_seqs(inseqs, blast_db=self.blast_db)
self.assertEqual(len(actual), 5)
# couple of sanity checks against command line blast
self.assertEqual(actual['s2_like_seq'][0][0]['SUBJECT ID'], 's2')
self.assertEqual(actual['s105'][0][2]['SUBJECT ID'], 's1')
def test_w_preexising_blastdb(self):
"""qiime_blast_seqs functions with pre-existing blast_db
"""
# pre-existing blast db
inseqs = MinimalFastaParser(self.inseqs1)
actual = qiime_blast_seqs(inseqs,blast_db=self.blast_db)
self.assertEqual(len(actual),5)
# couple of sanity checks against command line blast
self.assertEqual(actual['s2_like_seq'][0][0]['SUBJECT ID'],'s2')
self.assertEqual(actual['s105'][0][2]['SUBJECT ID'],'s1')
def test_alt_blast_param(self):
"""qiime_blast_seqs: alt blast params give alt results"""
# Fewer blast hits with stricter e-value
inseqs = MinimalFastaParser(self.inseqs1)
actual = qiime_blast_seqs(inseqs,
blast_db=self.blast_db,
params={'-e': '1e-4'})
# NOTE: A BUG (?) IN THE BlastResult OR THE PARSER RESULTS IN AN EXTRA
# BLAST RESULT IN THE DICT (actual HERE) WITH KEY ''
self.assertTrue('s2_like_seq' in actual)
self.assertFalse('s100' in actual)
def test_w_alt_seqs_per_blast_run(self):
"""qiime_blast_seqs: functions with alt seqs_per_blast_run
"""
for i in range(1, 20):
inseqs = MinimalFastaParser(self.inseqs1)
actual = qiime_blast_seqs(\
inseqs,blast_db=self.blast_db,seqs_per_blast_run=i)
self.assertEqual(len(actual), 5)
# couple of sanity checks against command line blast
self.assertEqual(actual['s2_like_seq'][0][0]['SUBJECT ID'], 's2')
self.assertEqual(actual['s105'][0][2]['SUBJECT ID'], 's1')
def test_w_alt_seqs_per_blast_run(self):
"""qiime_blast_seqs: functions with alt seqs_per_blast_run
"""
for i in range(1,20):
inseqs = MinimalFastaParser(self.inseqs1)
actual = qiime_blast_seqs(\
inseqs,blast_db=self.blast_db,seqs_per_blast_run=i)
self.assertEqual(len(actual),5)
# couple of sanity checks against command line blast
self.assertEqual(actual['s2_like_seq'][0][0]['SUBJECT ID'],'s2')
self.assertEqual(actual['s105'][0][2]['SUBJECT ID'],'s1')
def main():
option_parser, options, args = parse_command_line_parameters(**script_info)
blast_results = qiime_blast_seqs(
seqs=parse_fasta(open(options.input_fasta_fp)),
refseqs_fp=options.refseqs_fp,
seqs_per_blast_run=options.num_seqs_per_blast_run)
for query_id, blast_result in blast_results.items():
first_blast_result = blast_result[0][0]
print '%s: %s %s %s' % (query_id, first_blast_result['SUBJECT ID'],
first_blast_result['E-VALUE'],
first_blast_result['% IDENTITY'])
def main():
option_parser, options, args = parse_command_line_parameters(**script_info)
blast_results = qiime_blast_seqs(\
seqs=MinimalFastaParser(open(options.input_fasta_fp)),\
refseqs_fp=options.refseqs_fp,\
seqs_per_blast_run=options.num_seqs_per_blast_run)
for query_id, blast_result in blast_results.items():
first_blast_result = blast_result[0][0]
print '%s: %s %s %s' % (\
query_id,
first_blast_result['SUBJECT ID'],
first_blast_result['E-VALUE'],
first_blast_result['% IDENTITY'])
def main():
option_parser, options, args = parse_command_line_parameters(**script_info)
blast_results = qiime_blast_seqs(
seqs=parse_fasta(open(options.input_fasta_fp)),
refseqs_fp=options.refseqs_fp,
seqs_per_blast_run=options.num_seqs_per_blast_run,
)
for query_id, blast_result in blast_results.items():
first_blast_result = blast_result[0][0]
print "%s: %s %s %s %s %s" % (
query_id,
first_blast_result["SUBJECT ID"],
first_blast_result["E-VALUE"],
first_blast_result["% IDENTITY"],
# Start and end coordinates required to identify match orientation
first_blast_result["S. START"],
first_blast_result["S. END"],
)