# ---------------------------------------------------------------------------- # Copyright (c) 2016-2023, QIIME 2 development team. # # Distributed under the terms of the Modified BSD License. # # The full license is in the file LICENSE, distributed with this software. # ---------------------------------------------------------------------------- import os import tempfile from q2_types.feature_data import AlignedDNAFASTAFormat from q2_types.tree import NewickFormat from q2_phylogeny._raxml import run_command _iqtree_defaults = { 'seed': None, 'n_cores': 1, 'n_cores_max': None, 'n_runs': 1, 'substitution_model': 'MFP', 'run_prefix': 'q2iqtree', 'dtype': 'DNA', 'n_init_pars_trees': None, 'n_top_init_trees': None, 'n_best_retain_trees': None, 'n_iter': None, 'stop_iter': None, 'perturb_nni_strength': None, 'spr_radius': None, 'fast': False, 'alrt': None, 'abayes': False, 'lbp': None, 'allnni': False, 'bnni': False, 'safe': False, 'bootstrap_replicates': 1000, 'n_max_ufboot_iter': None, 'n_ufboot_steps': None, 'min_cor_ufboot': None, 'ep_break_ufboot': None, } def _build_iqtree_command( alignment, seed: int = _iqtree_defaults['seed'], n_cores: int = _iqtree_defaults['n_cores'], n_cores_max: int = _iqtree_defaults['n_cores_max'], n_runs: int = _iqtree_defaults['n_runs'], substitution_model: str = _iqtree_defaults['substitution_model'], run_prefix: str = _iqtree_defaults['run_prefix'], dtype: str = _iqtree_defaults['dtype'], n_init_pars_trees: int = _iqtree_defaults['n_init_pars_trees'], n_top_init_trees: int = _iqtree_defaults['n_top_init_trees'], n_best_retain_trees: int = _iqtree_defaults['n_best_retain_trees'], n_iter: int = _iqtree_defaults['n_iter'], stop_iter: int = _iqtree_defaults['stop_iter'], perturb_nni_strength: float = _iqtree_defaults['perturb_nni_strength'], spr_radius: int = _iqtree_defaults['spr_radius'], allnni: bool = _iqtree_defaults['allnni'], fast: bool = _iqtree_defaults['fast'], alrt: int = _iqtree_defaults['alrt'], abayes: bool = _iqtree_defaults['abayes'], lbp: int = _iqtree_defaults['lbp'], safe: bool = _iqtree_defaults['safe']): cmd = ['iqtree'] cmd += ['-st', str(dtype), '--runs', '%i' % n_runs, '-s', str(alignment), '-m', str(substitution_model), '-pre', str(run_prefix)] if n_cores == 'auto' and n_cores_max: cmd += ['-nt', 'AUTO', '--threads-max', '%i' % n_cores_max] elif n_cores == 'auto' and n_cores_max is None: cmd += ['-nt', 'AUTO'] else: cmd += ['-nt', '%i' % n_cores] if seed: cmd += ['-seed', '%i' % seed] if safe: cmd += ['-safe'] if fast: cmd += ['-fast'] if alrt: cmd += ['-alrt', '%i' % alrt] if abayes: cmd += ['-abayes'] if lbp: cmd += ['-lbp', '%i' % lbp] if allnni: cmd += ['-allnni'] if n_init_pars_trees: cmd += ['-ninit', '%i' % n_init_pars_trees] if n_top_init_trees: cmd += ['-ntop', '%i' % n_top_init_trees] if n_best_retain_trees: cmd += ['-nbest', '%i' % n_best_retain_trees] if n_iter: cmd += ['-n', '%i' % n_iter] if stop_iter: cmd += ['-nstop', '%i' % stop_iter] if perturb_nni_strength: cmd += ['-pers', '%f' % perturb_nni_strength] if spr_radius: cmd += ['-sprrad', '%i' % spr_radius] return cmd def iqtree( alignment: AlignedDNAFASTAFormat, seed: int = _iqtree_defaults['seed'], n_cores: int = _iqtree_defaults['n_cores'], n_cores_max: int = _iqtree_defaults['n_cores_max'], n_runs: int = _iqtree_defaults['n_runs'], substitution_model: str = _iqtree_defaults['substitution_model'], n_init_pars_trees: int = _iqtree_defaults['n_init_pars_trees'], n_top_init_trees: int = _iqtree_defaults['n_top_init_trees'], n_best_retain_trees: int = _iqtree_defaults['n_best_retain_trees'], n_iter: int = _iqtree_defaults['n_iter'], stop_iter: int = _iqtree_defaults['stop_iter'], perturb_nni_strength: float = _iqtree_defaults['perturb_nni_strength'], spr_radius: int = _iqtree_defaults['spr_radius'], allnni: bool = _iqtree_defaults['allnni'], fast: bool = _iqtree_defaults['fast'], alrt: int = _iqtree_defaults['alrt'], abayes: bool = _iqtree_defaults['abayes'], lbp: int = _iqtree_defaults['lbp'], safe: bool = _iqtree_defaults['safe'], ) -> NewickFormat: result = NewickFormat() with tempfile.TemporaryDirectory() as temp_dir: run_prefix = os.path.join(temp_dir, 'q2iqtree') cmd = _build_iqtree_command(alignment, seed=seed, n_cores=n_cores, n_cores_max=n_cores_max, n_runs=n_runs, substitution_model=substitution_model, run_prefix=run_prefix, n_init_pars_trees=n_init_pars_trees, n_top_init_trees=n_top_init_trees, n_best_retain_trees=n_best_retain_trees, n_iter=n_iter, stop_iter=stop_iter, perturb_nni_strength=perturb_nni_strength, spr_radius=spr_radius, allnni=allnni, fast=fast, alrt=alrt, abayes=abayes, lbp=lbp, safe=safe) run_command(cmd) tree_tmp_fp = os.path.join(temp_dir, '%s.treefile' % run_prefix) os.rename(tree_tmp_fp, str(result)) return result def _build_iqtree_ufbs_command( alignment, seed: int = _iqtree_defaults['seed'], n_cores: int = _iqtree_defaults['n_cores'], n_cores_max: int = _iqtree_defaults['n_cores_max'], n_runs: int = _iqtree_defaults['n_runs'], substitution_model: str = _iqtree_defaults['substitution_model'], bootstrap_replicates: int = _iqtree_defaults['bootstrap_replicates'], run_prefix: str = _iqtree_defaults['run_prefix'], dtype: str = _iqtree_defaults['dtype'], n_init_pars_trees: int = _iqtree_defaults['n_init_pars_trees'], n_top_init_trees: int = _iqtree_defaults['n_top_init_trees'], n_best_retain_trees: int = _iqtree_defaults['n_best_retain_trees'], stop_iter: int = _iqtree_defaults['stop_iter'], perturb_nni_strength: float = _iqtree_defaults['perturb_nni_strength'], spr_radius: int = _iqtree_defaults['spr_radius'], n_max_ufboot_iter: int = _iqtree_defaults['n_max_ufboot_iter'], n_ufboot_steps: int = _iqtree_defaults['n_ufboot_steps'], min_cor_ufboot: float = _iqtree_defaults['min_cor_ufboot'], ep_break_ufboot: float = _iqtree_defaults['ep_break_ufboot'], allnni: bool = _iqtree_defaults['allnni'], alrt: int = _iqtree_defaults['alrt'], abayes: bool = _iqtree_defaults['abayes'], lbp: int = _iqtree_defaults['lbp'], bnni: bool = _iqtree_defaults['bnni'], safe: bool = _iqtree_defaults['safe']): # This is a separate command becuase there are several # bootstrap specific options. cmd = ['iqtree', '-bb', '%i' % bootstrap_replicates] cmd += ['-st', str(dtype), '--runs', '%i' % n_runs, '-s', str(alignment), '-m', str(substitution_model), '-pre', str(run_prefix)] if n_cores == 'auto' and n_cores_max: cmd += ['-nt', 'AUTO', '--threads-max', '%i' % n_cores_max] elif n_cores == 'auto' and n_cores_max is None: cmd += ['-nt', 'AUTO'] else: cmd += ['-nt', '%i' % n_cores] if seed: cmd += ['-seed', '%i' % seed] if safe: cmd += ['-safe'] if allnni: cmd += ['-allnni'] if alrt: cmd += ['-alrt', '%i' % alrt] if abayes: cmd += ['-abayes'] if lbp: cmd += ['-lbp', '%i' % lbp] if bnni: cmd += ['-bnni'] if n_init_pars_trees: cmd += ['-ninit', '%i' % n_init_pars_trees] if n_top_init_trees: cmd += ['-ntop', '%i' % n_top_init_trees] if n_best_retain_trees: cmd += ['-nbest', '%i' % n_best_retain_trees] if stop_iter: cmd += ['-nstop', '%i' % stop_iter] if perturb_nni_strength: cmd += ['-pers', '%f' % perturb_nni_strength] if spr_radius: cmd += ['-sprrad', '%i' % spr_radius] if n_max_ufboot_iter: cmd += ['-nm', '%i' % n_max_ufboot_iter] if n_ufboot_steps: cmd += ['-nstep', '%i' % n_ufboot_steps] if min_cor_ufboot: cmd += ['-bcor', '%f' % min_cor_ufboot] if ep_break_ufboot: cmd += ['-beps', '%f' % ep_break_ufboot] return cmd def iqtree_ultrafast_bootstrap( alignment: AlignedDNAFASTAFormat, seed: int = _iqtree_defaults['seed'], n_cores: int = _iqtree_defaults['n_cores'], n_cores_max: int = _iqtree_defaults['n_cores_max'], n_runs: int = _iqtree_defaults['n_runs'], substitution_model: str = _iqtree_defaults['substitution_model'], bootstrap_replicates: int = _iqtree_defaults['bootstrap_replicates'], n_init_pars_trees: int = _iqtree_defaults['n_init_pars_trees'], n_top_init_trees: int = _iqtree_defaults['n_top_init_trees'], n_best_retain_trees: int = _iqtree_defaults['n_best_retain_trees'], stop_iter: int = _iqtree_defaults['stop_iter'], perturb_nni_strength: float = _iqtree_defaults['perturb_nni_strength'], spr_radius: int = _iqtree_defaults['spr_radius'], n_max_ufboot_iter: int = _iqtree_defaults['n_max_ufboot_iter'], n_ufboot_steps: int = _iqtree_defaults['n_ufboot_steps'], min_cor_ufboot: float = _iqtree_defaults['min_cor_ufboot'], ep_break_ufboot: float = _iqtree_defaults['ep_break_ufboot'], allnni: bool = _iqtree_defaults['allnni'], alrt: int = _iqtree_defaults['alrt'], abayes: bool = _iqtree_defaults['abayes'], lbp: int = _iqtree_defaults['lbp'], bnni: bool = _iqtree_defaults['bnni'], safe: bool = _iqtree_defaults['safe'] ) -> NewickFormat: # NOTE: the IQ-TREE commands `-n` (called as `n_iter` in the `iqtree` # method) and `-fast` are not compatable with ultrafast_bootstrap `-bb`. result = NewickFormat() with tempfile.TemporaryDirectory() as temp_dir: run_prefix = os.path.join(temp_dir, 'q2iqtreeufboot') cmd = _build_iqtree_ufbs_command( alignment, seed=seed, n_cores=n_cores, n_cores_max=n_cores_max, n_runs=n_runs, substitution_model=substitution_model, bootstrap_replicates=bootstrap_replicates, run_prefix=run_prefix, n_init_pars_trees=n_init_pars_trees, n_top_init_trees=n_top_init_trees, n_best_retain_trees=n_best_retain_trees, stop_iter=stop_iter, perturb_nni_strength=perturb_nni_strength, spr_radius=spr_radius, n_max_ufboot_iter=n_max_ufboot_iter, n_ufboot_steps=n_ufboot_steps, min_cor_ufboot=min_cor_ufboot, ep_break_ufboot=ep_break_ufboot, allnni=allnni, alrt=alrt, abayes=abayes, lbp=lbp, bnni=bnni, safe=safe) run_command(cmd) tree_tmp_fp = os.path.join(temp_dir, '%s.treefile' % run_prefix) os.rename(tree_tmp_fp, str(result)) return result