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304 lines
15 KiB
Python
304 lines
15 KiB
Python
#Author, date: Auden Cote-L'Heureux, last updated Aug 18th 2025 by AKG
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#Motivation: Select robust sequences from trees
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#Intent: Select clades of interest from large trees using taxonomic specifications
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#Dependencies: Python3, ete3, Biopython
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#Inputs: A folder containing: all PTLp2 output trees and all corresponding unaligned .fasta (pre-guidance) files
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#Outputs: A folder of grabbed clades and filtered unaligned fasta files
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#Example: python3 CladeGrabbing.py --input /Path/To/TreesandPreGuidance --target Sr_rh --min_presence 20
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#IMPORTANT: key parameters explained in "add_argument" section below
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#Dependencies
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import os, re, sys
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from Bio import SeqIO
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import ete3
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import argparse
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def get_args():
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parser = argparse.ArgumentParser(
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prog = 'Clade grabber, Version 2.1',
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description = "Updated Aug 1st, 2023 by Auden Cote-L'Heureux, modified by AKG Aug 18th 2025"
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)
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#add_argument section with parameters explained
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parser.add_argument('-i', '--input', type = str, required = True, help = 'Path to a folder containing input trees (which must have the file extension .tre, .tree, .treefile, or .nex)')
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parser.add_argument('-t', '--target', type = str, required = True, help = '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.')
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parser.add_argument('-m', '--min_presence', type = int, required = True, help = 'Minimum number of target taxa present in clade for it to be selected')
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parser.add_argument('-r', '--required_taxa', type = str, default = '', help = '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).')
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parser.add_argument('-nr', '--required_taxa_num', type = int, default = 0, help = 'The number of species belonging to taxa in the --required_taxa list that must be present in the clade. Default is 0.')
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parser.add_argument('-o', '--outgroup', type = str, default = '', help = '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 will be included as outgroups in the output unaligned fasta files (which will contain only sequences from a single selected clade, and all outgroup sequences in the tree captured by this argument).')
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parser.add_argument('-c', '--contaminants', type = float, default = 2, help = 'The number of non-ingroup contaminants allowed in a clade, or if less than 1 the proportion of sequences in a clade that can be non-ingroup (i.e. presumed contaminants). Default is to allow 2 contaminants.')
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parser.add_argument('-ft', '--first_target', type=str, default='', help='[Optional] A comma-separated list or .txt file of complete/partial taxon codes for an initial, broad clade search. If provided, the script will first find clades with these taxa before applying the main --target filter.')
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parser.add_argument('-fm', '--first_min_presence', type=int, default=0, help='[Optional] Minimum number of sequences from --first_target required in a clade for it to be used in the second-stage search. Ignored if --first_target is not provided.')
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return parser.parse_args()
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def get_newick(fname):
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newick = ''
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for line in open(fname):
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line = line.split(' ')[-1]
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if(line.startswith('(') or line.startswith('tree1=')):
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newick = line.split('tree1=')[-1].replace("'", '').replace('\\', '')
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return newick
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#This function reroots the tree on the largest Ba/Za clade. If there is no prokaryote clade,
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#it roots on the largest Op clade, then Pl, then Am, then Ex, then Sr.
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def reroot(tree):
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#This nested function returns the largest clade of a given taxonomic group
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def get_best_clade(taxon):
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best_size = 0; best_clade = []; seen_leaves = []
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#Traverse all nodes
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for node in tree.traverse('levelorder'):
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#If the node is big enough and not subsumed by a node we've already accepted
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if len(node) >= 3 and len(list(set(seen_leaves) & set([leaf.name for leaf in node]))) == 0:
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leaves = [leaf.name for leaf in node]
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#Create a record of leaves that belong to the taxonomic group
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target_leaves = set()
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for leaf in leaves[::-1]:
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if leaf[:2] in taxon:
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target_leaves.add(leaf[:10])
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leaves.remove(leaf)
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#If this clade is better than any clade we've seen before, grab it
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if len(target_leaves) > best_size and len(leaves) <= 2:
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best_clade = node
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best_size = len(target_leaves)
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seen_leaves.extend([leaf.name for leaf in node])
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return best_clade
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#Get the biggest clade for each taxonomic group (stops once it finds one)
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for taxon in [('Ba', 'Za'), ('Op'), ('Pl'), ('Am'), ('Ex'), ('Sr')]:
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clade = get_best_clade(taxon)
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if len([leaf for leaf in clade if leaf.name[:2] in taxon]) > 3:
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tree.set_outgroup( clade)
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break
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return tree
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def get_subtrees(args, file):
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newick = get_newick(args.input + '/' + file)
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tree = ete3.Tree(newick)
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majs = list(dict.fromkeys([leaf.name[:2] for leaf in tree]))
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# Only try to reroot trees with more than 2 major clades (original behavior)
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if len(majs) > 2:
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tree = reroot(tree)
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# -------------------------------
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# FIRST-STAGE (optional) FILTER
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# -------------------------------
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def get_outer_leafsets():
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"""
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Return a list of sets, each set = leaf names of an outer clade
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that passes --first_target, --first_min_presence, children_keep,
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and contaminants logic (using args.contaminants).
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If --first_target is not used, return one set containing ALL leaves.
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"""
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if not args.first_target or args.first_min_presence == 0:
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return [set(leaf.name for leaf in tree)] # no outer filter → whole tree
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# Parse first_target codes
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if '.' in args.first_target:
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first_target_codes = [l.strip() for l in open(args.first_target, 'r').readlines() if l.strip() != '']
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else:
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first_target_codes = [code.strip() for code in args.first_target.split(',') if code.strip() != '']
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outer_sets = []
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seen_leaves = []
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for node in tree.traverse('levelorder'):
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# large enough and not subsumed by already accepted outer node
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if len(node) >= args.first_min_presence and len(set(seen_leaves) & set([leaf.name for leaf in node])) == 0:
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leaves = [leaf.name for leaf in node]
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# children_keep logic but for first_target
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children_keep = 0
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for child in node.children:
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taken = False
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for code in first_target_codes:
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for leaf in child:
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if leaf.name.startswith(code):
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children_keep += 1
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taken = True
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break
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if taken:
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break
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if children_keep != len(node.children):
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continue
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# count first-target hits (use [:10] uniqueness like original)
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first_hits = set()
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for code in first_target_codes:
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for leaf in leaves[::-1]:
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if leaf.startswith(code):
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first_hits.add(leaf[:10])
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leaves.remove(leaf)
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# contaminants logic applied to FIRST-STAGE (reuse args.contaminants)
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passes_contam = ((args.contaminants < 1 and len(leaves) <= args.contaminants * len(first_hits)) or
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(args.contaminants >= 1 and len(leaves) <= args.contaminants))
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if len(first_hits) >= args.first_min_presence and passes_contam:
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outer_sets.append(set(leaf.name for leaf in node))
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seen_leaves.extend([leaf.name for leaf in node])
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return outer_sets
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# Build outer sets; if user supplied first-stage args, we'll restrict inner search to these
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using_first = bool(args.first_target) and args.first_min_presence > 0
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outer_leafsets = get_outer_leafsets()
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# --------------------------------
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# ORIGINAL INNER FILTER (unchanged)
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# --------------------------------
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# Getting a clean list of all target taxa
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if '.' in args.target:
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try:
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target_codes = [l.strip() for l in open(args.target, 'r').readlines() if l.strip() != '']
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except AttributeError:
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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')
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else:
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target_codes = [code.strip() for code in args.target.split(',') if code.strip() != '']
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# Getting a clean list of all "at least" taxa
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if '.' in args.required_taxa:
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try:
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required_taxa_codes = [l.strip() for l in open(args.required_taxa, 'r').readlines() if l.strip() != '']
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except AttributeError:
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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')
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else:
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required_taxa_codes = [code.strip() for code in args.required_taxa.split(',') if code.strip() != '']
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target_codes = list(dict.fromkeys(target_codes + required_taxa_codes))
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# Creating a record of selected subtrees, and all of the leaves in those subtrees
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selected_nodes = []; seen_leaves = []
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# Iterating through all nodes in tree, starting at "root" then working towards leaves
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for node in tree.traverse('levelorder'):
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# If using first-stage filter, only consider nodes fully inside some outer clade
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if using_first:
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node_leafs = set(leaf.name for leaf in node)
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# require subset (node fully contained in an accepted outer clade)
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if not any(node_leafs.issubset(S) for S in outer_leafsets):
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continue
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# If a node is large enough and is not contained in an already selected clade
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if len(node) >= args.min_presence and len(list(set(seen_leaves) & set([leaf.name for leaf in node]))) == 0:
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leaves = [leaf.name for leaf in node]
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# Accounting for cases where e.g. one child is a contaminant, and the other child is a good clade
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children_keep = 0
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for child in node.children:
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for code in target_codes:
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taken = False
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for leaf in child:
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if leaf.name.startswith(code):
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children_keep += 1
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taken = True
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break
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if taken:
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break
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if children_keep == len(node.children):
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target_leaves = set(); required_taxa_leaves = set()
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for code in target_codes:
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for leaf in leaves[::-1]:
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if leaf.startswith(code):
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target_leaves.add(leaf[:10])
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for req in required_taxa_codes:
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if leaf.startswith(req):
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required_taxa_leaves.add(leaf[:10])
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break
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leaves.remove(leaf)
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# Grab a clade as a subtree if it passes all filters
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if len(target_leaves) >= args.min_presence and len(required_taxa_leaves) >= args.required_taxa_num and ((args.contaminants < 1 and len(leaves) <= args.contaminants * len(target_leaves)) or len(leaves) <= args.contaminants):
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selected_nodes.append(node)
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seen_leaves.extend([leaf.name for leaf in node])
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# Write the subtrees to output .tre files
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for i, node in enumerate(selected_nodes[::-1]):
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with open('Subtrees/' + '.'.join(file.split('.')[:-1]) + '_' + str(i) + '.tre', 'w') as o:
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o.write(node.write())
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def make_new_unaligned(args):
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if not os.path.isdir('Subtrees_unaligned'):
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os.mkdir('Subtrees_unaligned')
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#Getting a clean list of outgroup taxa
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if '.' in args.outgroup:
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try:
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outgroup_codes = [l.strip() for l in open(args.outgroup, 'r').readlines() if l.strip() != '']
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except AttributeError:
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print('\n\nError: invalid "target" 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 will be included as outgroups in the output unaligned fasta files (which will contain only sequences from a single selected clade, and all outgroup sequences in the tree captured by this argument).\n\n')
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else:
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outgroup_codes = [code.strip() for code in args.outgroup.split(',') if code.strip() != '']
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for tree_file in os.listdir('Subtrees'):
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if tree_file.endswith('.tre'):
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og = tree_file[:10]
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tree = ete3.Tree('Subtrees/' + tree_file)
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#Get the fasta (aligned or unaligned, but if aligned not columns removed) for each subtree
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for f, file in enumerate(os.listdir(args.input)):
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if file.startswith(og) and file.split('.')[-1] in ('fa', 'faa', 'fna', 'fasta', 'fas'):
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with open('Subtrees_unaligned/' + tree_file.replace('.tre', '.fasta'), 'w') as o:
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#For all records in the fasta file
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for rec in SeqIO.parse(args.input + '/' + file, 'fasta'):
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keep = False
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#Keep it if it's in the outgroup taxa list
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for code in outgroup_codes:
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if rec.id.startswith(code):
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keep = True
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break
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#Or keep it if it's in the subtree
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if rec.description in [leaf.name for leaf in tree]:
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keep = True
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#Write the sequence to the output file if kept
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if keep:
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o.write('>' + rec.description + '\n' + str(rec.seq).replace('-', '') + '\n\n')
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break
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def main():
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args = get_args()
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if(not os.path.isdir('Subtrees')):
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os.mkdir('Subtrees')
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f = 0
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for file in os.listdir(args.input):
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if file.split('.')[-1] in ('tre', 'tree', 'treefile', 'nex'):
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print(str(f + 1) + '. ' + file)
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f += 1
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get_subtrees(args, file)
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make_new_unaligned(args)
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main()
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