Rhomboid proteases

Load the dataset

The loaded MSA has 2767 sequences and 135       positions.
After filtering, we have 135 remaining positions.
After filtering, we have 2767 remaining sequences.
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Number of effective sequences 1792

import numpy as np
from cocoatree.datasets import load_rhomboid_proteases
import cocoatree.msa as c_msa
import cocoatree.statistics.position as c_pos


dataset = load_rhomboid_proteases()

loaded_seqs = dataset["alignment"]
loaded_seqs_id = dataset["sequence_ids"]
n_loaded_pos, n_loaded_seqs = len(loaded_seqs[0]), len(loaded_seqs)

print(f"The loaded MSA has {n_loaded_seqs} sequences and {n_loaded_pos} \
      positions.")

sequences, sequences_id, positions = c_msa.filter_sequences(
    loaded_seqs, loaded_seqs_id, gap_threshold=0.4, seq_threshold=0.2)
n_pos = len(positions)
print(f"After filtering, we have {n_pos} remaining positions.")
print(f"After filtering, we have {len(sequences)} remaining sequences.")

seq_weights, m_eff = c_pos.compute_seq_weights(sequences)
print('Number of effective sequences %d' %
      np.round(m_eff))