def create_ref_bloom_filter(reference_file, error_rate, bf_file, format="fasta"):
"""From a given FASTA reference sequence creates a bloom filter file
from each read.
"""
if format == "fasta":
file_it = FastaIterator
record = lambda it: (seq.seq for seq in it)
elif format == "fastq":
file_it = FastqGeneralIterator
record = lambda it: (seq for _, seq, _ in it)
capacity = total_reads(reference_file)
with open(reference_file) as handle:
it = file_it(handle)
read_it = record(it)
read_len = 109
read_in = []
read = []
buffer = []
bf = BloomFilter(capacity, error_rate, bf_file)
sequence = read_it.next()
step = read_len
i = 0
while i < len(sequence):
read = sequence[i:i + read_len - 1]
i += step
print(read)
bf.update(read)
bf.close()
def create(infile, outfile, capacity: int, error_rate: float = 0.05):
import tqdm
import urllib
from pybloomfilter import BloomFilter
bf = BloomFilter(capacity, error_rate, outfile)
with open(infile) as f:
for _, word in enumerate(tqdm.tqdm(f, total=capacity)):
if "%" in word:
word = urllib.parse.unquote(word).lower()
word = word.rstrip()
bf.add(word)
bf.close()
def process(files):
#Iterate over the lines of all files listed in sys.argv[1:], defaulting to sys.stdin if the list is empty.
#If a filename is '-', it is also replaced by sys.stdin.
if os.path.isfile(bloomfile):
UNIQUES = BloomFilter.open(bloomfile)
else:
UNIQUES = BloomFilter(MAXUNIQUES, ACCUACY, bloomfile)
for record in fileinput.input(files):
record = str(record).strip()
if not record in UNIQUES:
UNIQUES.add(record)
print record
UNIQUES.sync()
UNIQUES.close()
def process(files):
#Iterate over the lines of all files listed in sys.argv[1:], defaulting to sys.stdin if the list is empty.
#If a filename is '-', it is also replaced by sys.stdin.
if os.path.isfile(bloomfile):
UNIQUES = BloomFilter.open(bloomfile)
else:
UNIQUES = BloomFilter(MAXUNIQUES, ACCUACY, bloomfile)
for record in fileinput.input(files):
record = str(record).strip()
if not record in UNIQUES:
UNIQUES.add(record)
print record
UNIQUES.sync()
UNIQUES.close()