def test_create_blast_from_file(self):
file_var = "NotExist"
e_var = 1e-50
batch_size = 20
outfile_var = "foolname"
setting = Setting()
setting.add_all(blast_e_value=e_var, blast_wdir=self.Blast_dir,
blast_infile=file_var, blast_outfile=outfile_var,
blast_batch_size=batch_size,
)
with self.assertRaises(IOError):
RunBlast.create_blast_from_file(setting_class=setting)
infile_var = self.Blast_dir + "bIn"
setting.add("blast_infile", infile_var)
blast = RunBlast.create_blast_from_file(setting)
self.assertEqual(blast.results, dict())
self.record_index = SeqIO.index(infile_var, "fasta")
for key in self.record_index:
# print key
self.assertEqual(str(self.record_index[key].seq), str(blast.record_index[key].seq))
self.assertEqual(str(self.record_index[key].id), str(blast.record_index[key].id))
self.assertEqual(blast.e_threshold, e_var)
self.assertEqual(blast.batch_size, batch_size)
def test_RunBlast_Batch(self):
self.e_threshold = 1e-50 # one of the default values on the website
try:
os.remove(self.Blast_dir + "AmiGO_Record.temp")
except IOError:
pass
blast = RunBlast(records=self.record_index, e_value=self.e_threshold,
wdir=self.Blast_dir, debug=False)
blast.run()
expected = dict({'lcl|AE014075.1_gene_1': set([]),
'lcl|AE014075.1_gene_2': set([]), # no result with filter 1e-50 #'GO:0004803', 'GO:0006313']),
'lcl|AE014075.1_gene_3': set([
'GO:0050661', 'GO:0016597', 'GO:0016310', 'GO:0005524', 'GO:0000166', 'GO:0055114', 'GO:0009088', 'GO:0004412', 'GO:0004072', 'GO:0009089', 'GO:0009090', 'GO:0009086', 'GO:0009067', 'GO:0006520', 'GO:0008152', 'GO:0008652', 'GO:0009507', 'GO:0016491', 'GO:0009570', 'GO:0006164', 'GO:0000023', 'GO:0019252', 'GO:0019761', 'GO:0043085', 'GO:0071470', 'GO:0005634', 'GO:0005737', 'GO:0009097', 'GO:0005575'
]),
'lcl|AE014075.1_gene_4': set([
'GO:0016310', 'GO:0005524', 'GO:0000166', 'GO:0004413', 'GO:0009088', 'GO:0005737'
]),
'lcl|AE014075.1_gene_5': set([
'GO:0030170', 'GO:0004795', 'GO:0009088', 'GO:0008652', 'GO:0005737', 'GO:0016829', 'GO:0006520', 'GO:0005634'
])
# Old list
# 'lcl|AE014075.1_gene_3': set(['GO:0071470', 'GO:0016310', 'GO:0005886', 'GO:0009067', 'GO:0000023', 'GO:0016597', 'GO:0043085', 'GO:0016491', 'GO:0005737', 'GO:0050661', 'GO:0040007', 'GO:0005618', 'GO:0009570', 'GO:0005634', 'GO:0006520', 'GO:0019877', 'GO:0000166', 'GO:0016740', 'GO:0009097', 'GO:0009090', 'GO:0019252', 'GO:0019761', 'GO:0016301', 'GO:0008152', 'GO:0009088', 'GO:0055114', 'GO:0009507', 'GO:0008652', 'GO:0005829', 'GO:0006555', 'GO:0004412', 'GO:0005575', 'GO:0009089', 'GO:0005524', 'GO:0006164', 'GO:0006531', 'GO:0009086', 'GO:0004072', 'GO:0009082']),
# 'lcl|AE014075.1_gene_4': set(['GO:0005737', 'GO:0006566', 'GO:0000394', 'GO:0016310', 'GO:0009617', 'GO:0004413', 'GO:0000166', 'GO:0019344', 'GO:0009620', 'GO:0009088', 'GO:0009570', 'GO:0009086', 'GO:0005524', 'GO:0009507']),
# 'lcl|AE014075.1_gene_5': set(['GO:0005125', 'GO:0016311', 'GO:0046360', 'GO:0003674', 'GO:0030170', 'GO:0004795', 'GO:0005737', 'GO:0006566', 'GO:0005615', 'GO:0005634', 'GO:0006520', 'GO:0005524', 'GO:0008150', 'GO:0070905', 'GO:0008152', 'GO:0009071', 'GO:0008652', 'GO:0006897', 'GO:0005829', 'GO:0005575', 'GO:0009088', 'GO:0004765', 'GO:0016829'])
})
for k, v in expected.items():
seq = blast.results[k]
self.assertEqual(v, seq.combined_terms, "Error in %s. \nExpected: %s\nActual: %s\n" %
(k, sorted(expected[k]), sorted(seq.combined_terms)))
def test_init_dict(self): # allterms, default_value=0)
expected = dict({"GO:01": 0,
"GO:03": 0,
"GO:04": 0,
"GO:05": 0,
})
new_dict = RunBlast(records=self.record_index, e_value=self.e_threshold,
wdir=self.Blast_dir, outfile="BlastOut")
default_dict = new_dict.init_dict(self.template_set_small, 0)
self.assertEqual(expected, default_dict)
def test_RunBlast(self):
blast = RunBlast(records=self.record_index, e_value=self.e_threshold, wdir=self.Blast_dir)
blast.run_single()
expected = dict({'lcl|AE014075.1_gene_1': set([]),
'lcl|AE014075.1_gene_2': set(['GO:0004803', 'GO:0006313']),
'lcl|AE014075.1_gene_3': set(['GO:0071470', 'GO:0016310', 'GO:0005886', 'GO:0009067', 'GO:0000023', 'GO:0016597', 'GO:0043085', 'GO:0016491', 'GO:0005737', 'GO:0050661', 'GO:0040007', 'GO:0005618', 'GO:0009570', 'GO:0005634', 'GO:0006520', 'GO:0019877', 'GO:0000166', 'GO:0016740', 'GO:0009097', 'GO:0009090', 'GO:0019252', 'GO:0019761', 'GO:0016301', 'GO:0008152', 'GO:0009088', 'GO:0055114', 'GO:0009507', 'GO:0008652', 'GO:0005829', 'GO:0006555', 'GO:0004412', 'GO:0005575', 'GO:0009089', 'GO:0005524', 'GO:0006164', 'GO:0006531', 'GO:0009086', 'GO:0004072', 'GO:0009082']),
'lcl|AE014075.1_gene_4': set(['GO:0005737', 'GO:0006566', 'GO:0000394', 'GO:0016310', 'GO:0009617', 'GO:0004413', 'GO:0000166', 'GO:0019344', 'GO:0009620', 'GO:0009088', 'GO:0009570', 'GO:0009086', 'GO:0005524', 'GO:0009507']),
'lcl|AE014075.1_gene_5': set(['GO:0005125', 'GO:0016311', 'GO:0046360', 'GO:0003674', 'GO:0030170', 'GO:0004795', 'GO:0005737', 'GO:0006566', 'GO:0005615', 'GO:0005634', 'GO:0006520', 'GO:0005524', 'GO:0008150', 'GO:0070905', 'GO:0008152', 'GO:0009071', 'GO:0008652', 'GO:0006897', 'GO:0005829', 'GO:0005575', 'GO:0009088', 'GO:0004765', 'GO:0016829'])
})
for k, v in expected.items():
seq = blast.results[k]
self.assertEqual(v, seq.combined_terms, "Error in %s" % k)
def test_update_counter_from_dictionaries(self):
# start with empty dictionary
new_Blast = RunBlast(records=self.record_index, e_value=self.e_threshold,
wdir=self.Blast_dir, outfile="BlastOut")
expected = dict({"GO:01": 1,
"GO:03": 2,
"GO:04": 2,
"GO:05": 1, })
new_dict = new_Blast.init_dict(self.template_set_small, 0)
new_Blast.update_counter_from_dictionaries(new_dict, self.template_set_small)
# print(new_dict)
self.assertEqual(expected, new_dict)
expected = dict({"GO:01": 3,
"GO:02": 1,
"GO:03": 2,
"GO:04": 2,
"GO:05": 2,
"GO:06": 1,
"GO:07": 1})
new_dict = new_Blast.init_dict(self.template_set, 0)
new_Blast.update_counter_from_dictionaries(new_dict, self.template_set)
self.assertEqual(expected, new_dict)
def test_RunBlast_subset(self):
sub_record = dict({'lcl|AE014075.1_gene_4': self.record_index['lcl|AE014075.1_gene_4'],
'lcl|AE014075.1_gene_5': self.record_index['lcl|AE014075.1_gene_5']
})
blast = RunBlast(records=sub_record, e_value=1e-200, wdir=self.Blast_dir)
blast.run_single()
expected = dict({'lcl|AE014075.1_gene_4': set([]),
# 'lcl|AE014075.1_gene_5':set(['GO:0004795', 'GO:0030170', 'GO:0009088'])
'lcl|AE014075.1_gene_5': set(['GO:0004795', 'GO:0009088'])
})
for k, v in expected.items():
seq = blast.results[k]
self.assertEqual(v, seq.combined_terms)
#
for k, v in blast.results.items():
print k, v.combined_terms
