def snp_gen():
for snp in snps:
# get SNP sequences
snp_1hot_list = bvcf.snp_seq1(snp, job['seq_length'], genome_open)
for snp_1hot in snp_1hot_list:
yield {'sequence': snp_1hot}
def snp_gen():
for snp in snps:
# get SNP sequences
snp_1hot_list = bvcf.snp_seq1(snp, params_model['seq_length'],
genome_open)
for snp_1hot in snp_1hot_list:
yield snp_1hot
def snps_next_batch(snps, snp_i, batch_size, seq_len, genome_open):
""" Load the next batch of SNP sequence 1-hot. """
batch_1hot = []
batch_snps = []
while len(batch_1hot) < batch_size and snp_i < len(snps):
# get SNP sequences
snp_1hot = bvcf.snp_seq1(snps[snp_i], seq_len, genome_open)
# if it was valid
if len(snp_1hot) > 0:
# accumulate
batch_1hot += snp_1hot
batch_snps.append(snps[snp_i])
# advance SNP index
snp_i += 1
# convert to array
batch_1hot = np.array(batch_1hot)
return batch_1hot, batch_snps, snp_i
def snp_gen():
for snp in snps:
# get SNP sequences
snp_1hot_list = bvcf.snp_seq1(snp, seq_length, genome_open)
for snp_1hot in snp_1hot_list:
yield snp_1hot