def test_rotating_ramifier(self):
stat_ram = StatisticalRam(31, 100)
stat_ram.add_kmers_from_file(KMER_TABLE)
centers = stat_ram.get_centers()
scales = stat_ram.get_scales()
rotation = stat_ram.get_rotation()
rotater = RotatingRamifier(31, 8, rotation, centers, scales)
rft = rotater.ramify('ATCGATCGATCGATCGATCGATCGATCGATC')
self.assertTrue(rft.shape == (8, ))
def calculate_pca_rotation(kmer_len, num_kmers, outfile, kmer_table):
"""Calculate a PCA rotation from a set of k-mers."""
stat_ram = StatisticalRam(kmer_len, num_kmers)
stat_ram.add_kmers_from_file(kmer_table)
out = {
'k': kmer_len,
'center': stat_ram.get_centers().tolist(),
'scale': stat_ram.get_scales().tolist(),
'rotation': stat_ram.get_rotation().tolist(),
}
outfile.write(dumps(out))
def __init__(self, queries, targets, **kwargs):
self.k = kwargs['k']
self.sub_ks = kwargs['sub_ks']
self.rft_dims = kwargs['rft_dims']
stat_ram = StatisticalRam(self.k, len(targets))
stat_ram.bulk_add_kmers(targets)
self.rotation = {
'center': stat_ram.get_centers(),
'scale': stat_ram.get_scales(),
'rotation': stat_ram.get_rotation(),
}
self.queries = queries
self.targets = targets
def calculate_pca_rotation_fasta(kmer_len, dropout, num_kmers, outfile,
fasta_list):
"""Calculate a PCA rotation from a set of k-mers."""
stat_ram = StatisticalRam(kmer_len, num_kmers)
fasta_list = [line.strip() for line in fasta_list]
with click.progressbar(fasta_list) as fastas:
for fasta_filename in fastas:
try:
stat_ram.fast_add_kmers_from_fasta(fasta_filename,
dropout=dropout)
except IndexError:
break
out = {
'k': kmer_len,
'center': stat_ram.get_centers().tolist(),
'scale': stat_ram.get_scales().tolist(),
'rotation': stat_ram.get_rotation().tolist(),
'num_kmers': stat_ram.num_kmers_added,
}
click.echo(f'Built rotation with {stat_ram.num_kmers_added:,} k-mers.',
err=True)
outfile.write(dumps(out))
def test_rotation(self):
stat_ram = StatisticalRam(31, 100)
stat_ram.add_kmers_from_file(KMER_TABLE)
rotation = stat_ram.get_rotation()
self.assertTrue(rotation.shape == (4 * 31, 4 * 31))
def test_scales(self):
stat_ram = StatisticalRam(31, 100)
stat_ram.add_kmers_from_file(KMER_TABLE)
scales = stat_ram.get_scales()
self.assertTrue(scales.shape == (4 * 31, ))