def iterative_adapter_prediction(fastq, ratios, kmer_lens,
sample_num, keep_len=12):
"""Return a list of predicted adapters.
Iteratively predict 3' adapter sequence with different
combinations of k and R.
"""
fq_seq = []
fq_obj = get_file_obj(fastq)
for i, s in enumerate(fastq_sequence(fq_obj)):
if i == sample_num:
break
fq_seq.append(s)
fq_obj.close()
collection = {}
for kmer_len in kmer_lens:
curated = {}
freq = count_kmers(fq_seq, kmer_len, sample_num)
for ratio in ratios:
clean = filter_kmers(freq, kmer_len, ratio)
assembl = assemble_kmers(clean, kmer_len//2)
for s, c in assembl:
key = s[:keep_len]
curated[key] = max(curated.get(key,0), c)
for s, c in curated.items():
collection[s] = round(collection.get(s,0)+c, 4)
asmbl_min_len = min(map(len, collection.keys()))
assembl = sorted(assemble_kmers(list(collection.items()), asmbl_min_len//2),
key=itemgetter(1), reverse=True)
return assembl
def adapter_prediction(fastq, ratio, kmer_len, sample_num):
"""Return a list of predicted adapters.
Predict 3' adapter sequence with a combination of k and R.
"""
fq_obj = get_file_obj(fastq)
fq_seq = fastq_sequence(fq_obj)
freq = count_kmers(fq_seq, kmer_len, sample_num)
clean = filter_kmers(freq, kmer_len, ratio)
assembl = sorted(assemble_kmers(clean, kmer_len//2),
key=itemgetter(1), reverse=True)
fq_obj.close()
return assembl
def adapter_prediction(fastq, ratio, kmer_len, sample_num):
"""Return a list of predicted adapters.
Predict 3' adapter sequence with a combination of k and R.
"""
fq_obj = get_file_obj(fastq)
fq_seq = fastq_sequence(fq_obj)
freq = count_kmers(fq_seq, kmer_len, sample_num)
clean = filter_kmers(freq, kmer_len, ratio)
assembl = sorted(assemble_kmers(clean, kmer_len // 2),
key=itemgetter(1),
reverse=True)
fq_obj.close()
return assembl
def iterative_adapter_prediction(fastq,
ratios,
kmer_lens,
sample_num,
keep_len=12):
"""Return a list of predicted adapters.
Iteratively predict 3' adapter sequence with different
combinations of k and R.
"""
fq_seq = []
fq_obj = get_file_obj(fastq)
for i, s in enumerate(fastq_sequence(fq_obj)):
if i == sample_num:
break
fq_seq.append(s)
fq_obj.close()
collection = {}
for kmer_len in kmer_lens:
curated = {}
freq = count_kmers(fq_seq, kmer_len, sample_num)
for ratio in ratios:
clean = filter_kmers(freq, kmer_len, ratio)
assembl = assemble_kmers(clean, kmer_len // 2)
for s, c in assembl:
key = s[:keep_len]
curated[key] = max(curated.get(key, 0), c)
for s, c in curated.items():
collection[s] = round(collection.get(s, 0) + c, 4)
asmbl_min_len = min(map(len, collection.keys()))
assembl = sorted(assemble_kmers(list(collection.items()),
asmbl_min_len // 2),
key=itemgetter(1),
reverse=True)
return assembl