def index_creation(test_kmers):
# 1_param = cobs.CompactIndexParameters()
#1_param.term_size = 1 # k-mer size
#1_param.clobber = True # overwrite output and temporary files
#1_param.false_positive_rate = 0.4 # higher false positive rate -> smaller index
for num in test_kmers:
ten_param = cobs.CompactIndexParameters()
ten_param.term_size = num # k-mer size
ten_param.clobber = True # overwrite output and temporary files
ten_param.false_positive_rate = 0.4 # higher false positive rate -> smaller index
cobs.compact_construct("/ten",
str(num) + "_" + "ten_index.cobs_compact",
index_params=ten_param)
#10_param = cobs.CompactIndexParameters()
#10_param.term_size = 1 # k-mer size
#10_param.clobber = True # overwrite output and temporary files
# 10_param.false_positive_rate = 0.4 # higher false positive rate -> smaller index
#1_param = cobs.CompactIndexParameters()
#1_param.term_size = 1 # k-mer size
#1_param.clobber = True # overwrite output and temporary files
#1_param.false_positive_rate = 0.4 # higher false positive rate -> smaller index
# cobs.compact_construct("/one", "one_index.cobs_compact")
# cobs.compact_construct("/hundred", "hundred_index.cobs_compact")
# cobs.compact_construct("/thousand", "thousand_index.cobs_compact")
return
def create_index(input_dir, output_dir, kmer_length, fpr):
""""Create cobs index"""
params = cobs.CompactIndexParameters()
params.term_size = kmer_length
params.clobber = True # overwrite output and temporary files
params.false_positive_rate = fpr # higher false positive rate -> smaller index
cobs.compact_construct(os.path.join(input_dir), os.path.join(output_dir) + str(kmer_length) + "_index_index.cobs_compact", index_params=params)
sys.exit(0)
def create_indexes_from_kmers(directory):
test_kmers = [1, 2, 5, 10, 15, 20]
for kmer in test_kmers:
params = cobs.CompactIndexParameters()
params.term_size = kmer
params.clobber = True # overwrite output and temporary files
params.false_positive_rate = 0.4 # higher false positive rate -> smaller index
cobs.compact_construct(directory,
"indexes/" + str(kmer) + "_index.cobs_compact",
index_params=params)
return test_kmers
def test_compact_construct_query(self):
index_file = datadir + "/python_test.cobs_compact"
# construct compact index
p = cobs.CompactIndexParameters()
p.clobber = True
cobs.compact_construct(input=datadir + "/fasta",
out_file=index_file,
index_params=p)
self.assertTrue(os.path.isfile(index_file))
# run queries
s = cobs.Search(index_file)
r = s.search("AGTCAACGCTAAGGCATTTCCCCCCTGCCTCCTGCCTGCTGCCAAGCCCT")
#print(r)
self.assertEqual(len(r), 7)
self.assertEqual(r[0].doc_name, "sample1")
self.assertEqual(r[0].score, 20)
for x in range(len(protein_file)):
hundred_thousand_indexes.append(x)
proteins = []
gene_names = []
for protein in hundred_thousand_indexes:
info = cleaned[protein]
proteins.append(info)
gene_names.append(titles[protein])
duplicate_set = set()
duplicate_count = 1
for prot_index in tqdm(range(len(hundred_thousand_indexes))):
info = proteins[prot_index]
if not gene_names[prot_index] in duplicate_set:
thou = open("FILES/" + gene_names[prot_index] + ".txt", "w")
thou.write(info)
thou.close()
duplicate_set.add(gene_names[prot_index])
else:
thou = open("FILES/" + gene_names[prot_index] + ";" + str(duplicate_count) + ".txt", "w")
thou.write(info)
thou.close()
duplicate_count += 1
params = cobs.CompactIndexParameters()
params.term_size = 10
params.clobber = True # overwrite output and temporary files
params.false_positive_rate = 0.01 # higher false positive rate -> smaller index
cobs.compact_construct("FILES/", "INDEX/" + "10_index_index.cobs_compact", index_params=params)