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Auden Cote-L'Heureux 2024-02-07 11:23:49 -05:00 committed by GitHub
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PTL2/Scripts/contamination.py
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@ -1,8 +1,12 @@
#Updated by ACL on 1/16 to fix subsisters
import os, sys, re import os, sys, re
from Bio import SeqIO from Bio import SeqIO
import ete3 import ete3
import guidance import guidance
import trees import trees
from statistics import mean
def get_newick(fname): def get_newick(fname):
@ -67,74 +71,114 @@ def get_subtrees(args, file):
except: except:
print('\nUnable to re-root the tree ' + file + ' (maybe it had only 1 major clade, or an inconvenient polytomy). Skipping this step and continuing to try to grab robust clades from the tree.\n') print('\nUnable to re-root the tree ' + file + ' (maybe it had only 1 major clade, or an inconvenient polytomy). Skipping this step and continuing to try to grab robust clades from the tree.\n')
#Getting a clean list of all target taxa exceptions = []
if os.path.isfile(args.target): if args.clade_grabbing_exceptions != None:
try: if os.path.isfile(args.clade_grabbing_exceptions):
target_codes = [l.strip() for l in open(args.target).readlines() if l.strip() != ''] exceptions = [line.strip() for line in open(args.clade_grabbing_exceptions)]
except AttributeError: else:
print('\n\nError: invalid "target" argument. This must be a comma-separated list of any number of digits/characters to describe focal taxa (e.g. Sr_ci_S OR Am_t), or a file with the extension .txt containing a list of complete or partial taxon codes. All sequences containing the complete/partial code will be identified as belonging to target taxa.\n\n') print('\nError: it looks like you tried to input a clade grabbing exceptions file, but it could not be found.\n')
else: exit()
#make sure that this is how nargs works
target_codes = [code.strip() for code in args.target if code.strip() != '']
#Getting a clean list of all "at least" taxa rules_per_clade = []
if os.path.isfile(args.required_taxa): if args.clade_grabbing_rules_file != None:
try: if os.path.isfile(args.clade_grabbing_rules_file):
at_least_codes = [l.strip() for l in open(args.required_taxa).readlines() if l.strip() != ''] lines = [line.strip().split('\t') for line in open(args.clade_grabbing_rules_file) if len(line.strip().split('\t')) == 5]
except AttributeError:
print('\n\nError: invalid "required_taxa" argument. This must be a comma-separated list of any number of digits/characters (e.g. Sr_ci_S OR Am_t), or a file with the extension .txt containing a list of complete or partial taxon codes, to describe taxa that MUST be present in a clade for it to be selected (e.g. you may want at least one whole genome).\n\n')
else:
#make sure that this is how nargs works
at_least_codes = [code.strip() for code in args.required_taxa if code.strip() != '']
target_codes = list(dict.fromkeys(target_codes + at_least_codes)) for line in lines:
if line[4].lower() == 'na':
rules_per_clade.append({ 'target_taxa' : line[0], 'num_contams' : int(line[1]), 'min_target_presence' : int(line[2]), 'required_taxa' : line[3], 'required_taxa_num' : 0 })
else:
rules_per_clade.append({ 'target_taxa' : line[0], 'num_contams' : int(line[1]), 'min_target_presence' : int(line[2]), 'required_taxa' : line[3], 'required_taxa_num' : int(line[4]) })
else:
print('\nError: it looks like you tried to input a clade grabbing rules file, but it could not be found.\n')
exit()
else:
rules_per_clade.append({ 'target_taxa' : args.target_taxa, 'num_contams' : args.num_contams, 'min_target_presence' : args.min_target_presence, 'required_taxa' : args.required_taxa, 'required_taxa_num' : args.required_taxa_num })
for clade in rules_per_clade:
if os.path.isfile(clade['target_taxa']):
try:
clade['target_taxa'] = [l.strip() for l in open(clade['target_taxa']).readlines() if l.strip() != '']
except AttributeError:
print('\nError: invalid "target_taxa" input (' + clade['target_taxa'] + '). This must be a comma-separated list of any number of digits/characters to describe focal taxa (e.g. Sr_ci_S,Am_t), or a file with the extension .txt containing a list of complete or partial taxon codes. All sequences containing the complete/partial code will be identified as belonging to target taxa.\n')
exit()
else:
clade['target_taxa'] = [code.strip() for code in clade['target_taxa'].split(',') if code.strip() != '']
if clade['required_taxa'] != None:
if os.path.isfile(clade['required_taxa']):
try:
clade['required_taxa'] = [l.strip() for l in open(clade['required_taxa']).readlines() if l.strip() != '']
except AttributeError:
print('\nError: invalid "required_taxa" argument. This must be a comma-separated list of any number of digits/characters (e.g. Sr_ci_S,Am_t), or a file with the extension .txt containing a list of complete or partial taxon codes, to describe taxa that MUST be present in a clade for it to be selected (e.g. you may want at least one whole genome).\n')
else:
clade['required_taxa'] = [code.strip() for code in clade['required_taxa'].split(',') if code.strip() != '' and code.strip().lower() != 'na']
clade['target_taxa'] = clade['target_taxa'] + clade['required_taxa']
else:
clade['required_taxa'] = []
#Creating a record of selected subtrees, and all of the leaves in those subtrees #Creating a record of selected subtrees, and all of the leaves in those subtrees
selected_nodes = []; seen_leaves = [] selected_leaves = []
#Iterating through all nodes in tree, starting at "root" then working towards leaves for clade in rules_per_clade:
for node in tree.traverse('levelorder'): seen_leaves = []
#If a node is large enough and is not contained in an already selected clade
if len(node) >= args.min_target_presence and len(list(set(seen_leaves) & set([leaf.name for leaf in node]))) == 0:
leaves = [leaf.name for leaf in node]
#Accounting for cases where e.g. one child is a contaminant, and the other child is a good clade with 1 fewer than the max number of contaminants #Iterating through all nodes in tree, starting at "root" then working towards leaves
children_keep = 0 for node in tree.traverse('levelorder'):
for child in node.children: #If a node is large enough and is not contained in an already selected clade
for code in target_codes: if len(node) >= clade['min_target_presence'] and len(list(set(seen_leaves) & set([leaf.name for leaf in node]))) == 0:
for leaf in child: leaves = [leaf.name for leaf in node]
if leaf.name.startswith(code):
children_keep += 1 #Accounting for cases where e.g. one child is a contaminant, and the other child is a good clade with 1 fewer than the max number of contaminants
children_keep = 0
for child in node.children:
for code in clade['target_taxa']:
taken = False
for leaf in child:
if leaf.name.startswith(code):
children_keep += 1
taken = True
break
if taken:
break break
if children_keep == len(node.children): if children_keep == len(node.children):
#Creating a record of all leaves belonging to the target/"at least" group of taxa, and any other leaves are contaminants
target_leaves = set(); at_least_leaves = set()
for code in target_codes:
for leaf in leaves[::-1]:
if leaf.startswith(code):
target_leaves.add(leaf[:10])
if code in at_least_codes: #Creating a record of all leaves belonging to the target/"at least" group of taxa, and any other leaves are contaminants
at_least_leaves.add(leaf[:10]) target_leaves = set(); at_least_leaves = set(); target_leaves_full_names = []
for code in clade['target_taxa']:
for leaf in leaves[::-1]:
if leaf.startswith(code):
target_leaves.add(leaf[:10])
target_leaves_full_names.append(leaf)
leaves.remove(leaf) for req in clade['required_taxa']:
if leaf.startswith(req):
at_least_leaves.add(leaf[:10])
break
#Grab a clade as a subtree if 1) it has enough target taxa; 2) it has enough "at least" taxa; 3) it does not have too many contaminants leaves.remove(leaf)
if len(target_leaves) >= args.min_target_presence and len(at_least_leaves) >= args.n_at_least and ((args.contaminants < 1 and len(leaves) < args.contaminants * len(target_leaves)) or len(leaves) < args.contaminants):
selected_nodes.append(node)
seen_leaves.extend([leaf.name for leaf in node])
#Write the subtrees to output .tre files #Grab a clade as a subtree if 1) it has enough target taxa; 2) it has enough "at least" taxa; 3) it does not have too many contaminants
seqs2keep = [leaf.name for node in selected_nodes for leaf in node] if len(target_leaves) >= clade['min_target_presence'] and len(at_least_leaves) >= clade['required_taxa_num'] and ((clade['num_contams'] < 1 and len(leaves) <= clade['num_contams'] * len(target_leaves)) or len(leaves) <= clade['num_contams']):
selected_leaves.extend(target_leaves_full_names)
seen_leaves.extend([leaf.name for leaf in node])
all_clades = [clade for group in rules_per_clade for clade in group['target_taxa']]
seqs2keep = [leaf.name for leaf in tree if leaf.name in selected_leaves or not any([leaf.name.startswith(clade) for clade in all_clades]) or any([leaf.name.startswith(ex) for ex in exceptions])]
return seqs2keep return seqs2keep
def get_sisters(args, file, contam_per_tax): def get_sisters(args, file, sister_contam_per_tax, subsister_contam_per_tax):
seqs2remove = [] seqs2remove = []
#Read the tree using ete3 and reroot it using the above function #Read the tree using ete3 and reroot it using the above function
newick = get_newick(file) newick = get_newick(file)
tree = ete3.Tree(newick) tree = ete3.Tree(newick)
@ -144,54 +188,126 @@ def get_sisters(args, file, contam_per_tax):
except: except:
print('\nUnable to re-root the tree ' + file + ' (maybe it had only 1 major clade, or an inconvenient polytomy). Skipping this step and continuing to try to grab robust clades from the tree.\n') print('\nUnable to re-root the tree ' + file + ' (maybe it had only 1 major clade, or an inconvenient polytomy). Skipping this step and continuing to try to grab robust clades from the tree.\n')
mean_bl = mean([leaf.dist for leaf in tree])
all_taxa_in_tree = [leaf.name[:10] for leaf in tree]
coconts = { }
if args.cocontaminants != None:
if os.path.isfile(args.cocontaminants):
for line in open(args.cocontaminants):
line = line.strip().split('\t')
if len(line) == 2:
if line[0] in all_taxa_in_tree:
coconts.update({ line[0] : line[1] })
else:
print('\nERROR: It looks like you tried to input a co-contaminants file to the contamination loop, but the file could not be found.\n')
exit()
for tax in all_taxa_in_tree:
if tax not in coconts:
coconts.update({ tax : tax })
#For each sequence #For each sequence
for leaf in tree: for leaf in tree:
bad_sisters = { contam[0] : contam[1] for tax in sister_contam_per_tax for contam in sister_contam_per_tax[tax] if leaf.name.startswith(tax) }
bad_subsisters = [contam for tax in subsister_contam_per_tax for contam in subsister_contam_per_tax[tax] if leaf.name.startswith(tax)]
#This loop will keep moving towards the root of the tree until it finds a node that if len(bad_sisters) > 0 or len(bad_subsisters) > 0:
#has leaves from a cell other than the one for which we are looking for sisters #This loop will keep moving towards the root of the tree until it finds a node that
parent_node = leaf; sister_taxa = {leaf.name[:10]} #has leaves from a cell other than the one for which we are looking for sisters
while len(sister_taxa) == 1: parent_node = leaf; seen_taxa = {coconts[leaf.name[:10]]}; sisters = []
parent_node = parent_node.up while len(seen_taxa) == 1:
for l2 in parent_node: parent_node = parent_node.up
sister_taxa.add(l2.name[:10])
#Create a record of the sister sequences for l2 in parent_node:
sisters = list(dict.fromkeys([sister for sister in parent_node if sister.name[:10] != leaf.name[:10]])) seen_taxa.add(coconts[l2.name[:10]])
if coconts[l2.name[:10]] != coconts[leaf.name[:10]]:
sisters.append(l2.name[:10])
bad_sisters = list(dict.fromkeys([contam for tax in contam_per_tax for contam in contam_per_tax[tax] if leaf.name.startswith[tax]])) #Create a record of the subsister sequences
sub_sisters = []
if args.subsister_rules != None:
new_parent_node = parent_node.up
sisters_removable = [] for l2 in new_parent_node:
for contam in bad_sisters: if l2.name not in [l.name for l in parent_node]:
for sister in sisters: sub_sisters.append(l2.name)
if sister.startswith(contam) and sister not in sisters_removable:
sisters_removable.append(sister) #Create a record of the sister sequences
sisters = list(dict.fromkeys(sisters))
if len(sisters_removable) == len(sisters):
seqs2remove.append(leaf.name) sisters_removable = []; bls = []
for contam in bad_sisters:
for sister in sisters:
if sister.startswith(contam) and sister not in sisters_removable:
sisters_removable.append(sister)
bls.append(bad_sisters[contam])
subsisters_removable = []
for contam in bad_subsisters:
for sub_sister in sub_sisters:
if sub_sister.startswith(contam) and sub_sister not in subsisters_removable:
subsisters_removable.append(sub_sister)
if len(bls) > 0:
bl_rule_min = min(bls)
else:
bl_rule_min = 0
if len(sisters_removable) == len(sisters) and leaf.dist <= bl_rule_min*mean_bl and len(sisters_removable) > 0:
seqs2remove.append(leaf.name)
elif len(subsisters_removable) == len(sub_sisters) and len(subsisters_removable) > 0:
seqs2remove.append(leaf.name)
return [leaf.name for leaf in tree if leaf.name not in seqs2remove] return [leaf.name for leaf in tree if leaf.name not in seqs2remove]
def write_new_preguidance(params, seqs2keep, seqs_per_og, tree_file):
def write_new_preguidance(params, seqs2keep, seqs_per_og): if params.cl_exclude_taxa != None:
try:
exclude_taxa = list(dict.fromkeys([line.strip() for line in open(params.cl_exclude_taxa)]))
except (FileNotFoundError, TypeError) as e:
print('\nERROR: Unable to read the file listing taxa to exclude in the first iteration of the contamination loop (--cl_exclude_taxa). Please make sure that the path is correct and that the file is formatted correctly.\n\n' + str(e) + '\n')
exit()
else:
exclude_taxa = []
prefix = '.'.join(tree_file.split('.')[:-1]) prefix = tree_file.split('.')[0]
seq_file = [file for file in seqs_per_og if file.startswith(prefix)] seq_file = [file for file in seqs_per_og if file.startswith(prefix)]
if len(seq_file) == 0:
seq_file = [file for file in seqs_per_og if file.startswith(prefix.split('.')[0])]
if len(seq_file) == 0: if len(seq_file) == 0:
print('\nNo sequence file found for tree file ' + tree_file + '. Skipping this gene family.\n') print('\nNo sequence file found for tree file ' + tree_file + '. Skipping this gene family.\n')
elif len(seq_file) > 1: return None, []
print('\nMore than one sequence file found matching the tree file ' + tree_file + '. Please make your file names more unique: there should be one sequence file for every tree file, with a matching unique prefix (everything before the first "."). Skipping this gene family.\n') elif len(seq_file) > 1:
print('\nMore than one sequence file found matching the tree file ' + tree_file + '. Please make your file names more unique: there should be one sequence file for every tree file, with a matching unique prefix (everything before the first "."). Skipping this gene family.\n')
if len(seq_file) == 1: return None, []
with open(params.output + '/Pre-Guidance/' + seq_file, 'w') as o: elif len(seq_file) == 1:
for rec in seqs_per_og[seq_file]: with open(params.output + '/Output/Pre-Guidance/' + seq_file[0], 'w') as o:
if rec in seqs2keep: for rec in seqs_per_og[seq_file[0]]:
o.write('>' + rec + '\n' + seqs_per_og[seq_file][rec] + '\n\n') if rec in seqs2keep and rec[:10] not in exclude_taxa and rec[:2] not in exclude_taxa and rec[:5] not in exclude_taxa:
na o.write('>' + rec + '\n' + seqs_per_og[seq_file[0]][rec] + '\n\n')
seqs_removed_from_og = [seq for seq in seqs_per_og[seq_file] if seq not in seqs2keep]
seqs_removed_from_og = [seq for seq in seqs_per_og[seq_file[0]] if seq not in seqs2keep]
return seq_file[0], seqs_removed_from_og
def cl_mafft(params):
for file in os.listdir(params.output + '/Output/Pre-Guidance'):
if file.split('.')[-1] in ('fasta', 'fas', 'faa'):
os.system('mafft ' + params.output + '/Output/Pre-Guidance/' + file + ' > ' + params.output + '/Output/NotGapTrimmed/' + file)
os.system('Scripts/trimal-trimAl/source/trimal -in ' + params.output + '/Output/NotGapTrimmed/' + file + ' -out ' + params.output + '/Output/Guidance/' + file.split('.')[0] + '.95gapTrimmed.fasta' + ' -gapthreshold 0.05 -fasta')
def cl_fasttree(params):
for file in os.listdir(params.output + '/Output/Guidance'):
if file.split('.')[-1] in ('fasta', 'fas', 'faa'):
os.system('FastTree ' + params.output + '/Output/Guidance/' + file + ' > ' + params.output + '/Output/Trees/' + file.split('.')[0] + '.FastTree.tre')
def run(params): def run(params):
@ -199,58 +315,107 @@ def run(params):
seqs_removed = [] seqs_removed = []
completed_ogs = [] completed_ogs = []
with open('SequencesRemoved_ContaminationLoop.txt', 'w') as o:
o.write('Sequence\tLoopRemoved\n')
for loop in range(params.nloops): for loop in range(params.nloops):
seqs_removed_loop = []
if params.start == 'raw': if params.start == 'raw':
seqs_per_og = { file : { rec.id : str(rec.seq) for rec in SeqIO.parse(file, 'fasta') } for file in os.listdir(params.output + '/Output/Pre-Guidance') if file.split('.')[-1] in ('fasta', 'fas', 'faa') } seqs_per_og = { file : { rec.id : str(rec.seq) for rec in SeqIO.parse(params.output + '/Output/Pre-Guidance/' + file, 'fasta') } for file in os.listdir(params.output + '/Output/Pre-Guidance') if file.split('.')[-1] in ('fasta', 'fas', 'faa') }
elif params.start in ('unaligned', 'aligned', 'trees'): elif params.start in ('unaligned', 'aligned', 'trees'):
seqs_per_og = { file : { rec.id : str(rec.seq).replace('-', '') for rec in SeqIO.parse(file, 'fasta') } for file in os.listdir(params.data) if file.split('.')[-1] in ('fasta', 'fas', 'faa') } seqs_per_og = { file : { rec.id : str(rec.seq).replace('-', '') for rec in SeqIO.parse(params.data + '/' + file, 'fasta') } for file in os.listdir(params.data) if file.split('.')[-1] in ('fasta', 'fas', 'faa') }
if loop == 0:
for file in os.listdir(params.data):
if file.split('.')[-1] in ('tre', 'tree', 'treefile'):
os.system('cp ' + params.data + '/' + file + ' ' + params.output + '/Output/Trees')
if loop > 0 or params.start == 'raw': if loop > 0 or params.start == 'raw':
os.system('mv ' + params.output + '/Pre-Guidance ' + params.output + '/Pre-Guidance_' + str(loop)) os.system('mv ' + params.output + '/Output/Pre-Guidance ' + params.output + '/Output/Pre-Guidance_' + str(loop))
os.mkdir(params.output + '/Pre-Guidance') os.mkdir(params.output + '/Output/Pre-Guidance')
if params.contamination_loop == 'clade': if params.contamination_loop == 'clade':
for tree_file in params.output + '/Trees': for tree_file in os.listdir(params.output + '/Output/Trees'):
if tree_file.split('.')[-1] in ('tre', 'tree', 'treefile', 'nex') and tree_file not in completed_ogs: if tree_file.split('.')[-1] in ('tre', 'tree', 'treefile', 'nex') and tree_file not in completed_ogs:
seqs2keep = get_subtrees(params, params.output + '/Trees/' + tree_file) seqs2keep = get_subtrees(params, params.output + '/Output/Trees/' + tree_file)
seqs_removed_from_og = write_new_preguidance(params, seqs2keep, seqs_per_og) seq_file, seqs_removed_from_og = write_new_preguidance(params, seqs2keep, seqs_per_og, tree_file)
if len(seqs_removed_from_og) == 0: if len(seqs_removed_from_og) == 0:
completed_ogs.append(tree_file) completed_ogs.append(tree_file)
else: else:
seqs_removed += [seq for seq in seqs_per_og[seq_file] if seq not in seqs2keep] seqs_removed_loop += [seq for seq in seqs_per_og[seq_file] if seq not in seqs2keep and seq not in seqs_removed]
elif params.contamination_loop == 'seq': elif params.contamination_loop == 'seq':
contam_per_tax = { line.strip().split('\t')[0] : line.strip().split('\t')[1:] for line in params.sister_rules }
if params.contamination_loop == 'clade': sister_contam_per_tax = { }
for tree_file in params.output + '/Trees': if params.sister_rules != None:
if tree_file.split('.')[-1] in ('tre', 'tree', 'treefile', 'nex') and tree_file not in completed_ogs: for line in open(params.sister_rules):
seqs2keep = get_sisters(params, params.output + '/Trees/' + tree_file, contam_per_tax) if line.strip().split('\t')[0] not in sister_contam_per_tax:
sister_contam_per_tax.update({ line.strip().split('\t')[0] : [] })
seqs_removed_from_og = write_new_preguidance(params, seqs2keep, seqs_per_og) try:
sister_contam_per_tax[line.strip().split('\t')[0]].append((line.strip().split('\t')[1], float(line.strip().split('\t')[2])))
except ValueError:
sister_contam_per_tax[line.strip().split('\t')[0]].append((line.strip().split('\t')[1], float('inf')))
except IndexError:
if line.strip() != '':
print('\nWarning: the line "' + line.strip() + '" in the sister rules file could not be processed\n')
if len(seqs_removed_from_og) == 0: subsister_contam_per_tax = { }
completed_ogs.append(tree_file) if params.subsister_rules != None:
else: if os.path.isfile(params.subsister_rules):
seqs_removed += [seq for seq in seqs_per_og[seq_file] if seq not in seqs2keep] for line in open(params.subsister_rules):
if line.strip().split('\t')[0] not in subsister_contam_per_tax and len(line.strip().split('\t')) == 2:
subsister_contam_per_tax.update({ line.strip().split('\t')[0] : [] })
os.system('mv ' + params.output + '/Trees ' + params.output + '/Trees_' + str(loop)) subsister_contam_per_tax[line.strip().split('\t')[0]].append(line.strip().split('\t')[1])
os.mkdir(params.output + '/Trees') else:
print('\nERROR: It looks like you tried to input a sub-sister rules file to the contamination loop, but the file could not be found.\n')
exit()
os.system('mv ' + params.output + '/Guidance ' + params.output + '/Guidance_' + str(loop)) for tree_file in os.listdir(params.output + '/Output/Trees'):
os.mkdir(params.output + '/Guidance') if tree_file.split('.')[-1] in ('tre', 'tree', 'treefile', 'nex') and tree_file not in completed_ogs:
seqs2keep = get_sisters(params, params.output + '/Output/Trees/' + tree_file, sister_contam_per_tax, subsister_contam_per_tax)
seq_file, seqs_removed_from_og = write_new_preguidance(params, seqs2keep, seqs_per_og, tree_file)
if len(seqs_removed_from_og) == 0:
completed_ogs.append(tree_file)
else:
seqs_removed_loop += [seq for seq in seqs_per_og[seq_file] if seq not in seqs2keep and seq not in seqs_removed]
seqs_removed += seqs_removed_loop
with open(params.output + '/Output/SequencesRemoved_ContaminationLoop.txt', 'a') as o:
for seq in seqs_removed_loop:
o.write(seq + '\t' + str(loop) + '\n')
os.system('mv ' + params.output + '/Output/Trees ' + params.output + '/Output/Trees_' + str(loop))
os.mkdir(params.output + '/Output/Trees')
os.system('mv ' + params.output + '/Output/Guidance ' + params.output + '/Output/Guidance_' + str(loop))
os.mkdir(params.output + '/Output/Guidance')
os.system('mv ' + params.output + '/Output/NotGapTrimmed ' + params.output + '/Output/NotGapTrimmed_' + str(loop))
os.mkdir(params.output + '/Output/NotGapTrimmed')
params.start = 'unaligned' params.start = 'unaligned'
params.end = 'trees' params.end = 'trees'
params.tree_method = params.cl_tree_method
guidance.run(params) if params.cl_alignment_method == 'mafft_only':
trees.run(params) cl_mafft(params)
else:
guidance.run(params)
with open('SequencesRemoved_ContaminationLoop.txt', 'w') as o: if params.cl_tree_method == 'fasttree':
for seq in seqs_removed: cl_fasttree(params)
o.write(seq + '\n') else:
if 'iqtree' in params.cl_tree_method:
os.system('rm -r ' + params.output + '/Output/Intermediate/IQTree/*')
elif params.cl_tree_method == 'raxml':
os.system('rm -r ' + params.output + '/Output/Intermediate/RAxML/*')
trees.run(params)