mirror of
http://43.156.76.180:8026/YuuMJ/EukPhylo.git
synced 2025-12-28 05:00:24 +08:00
Delete CladeGrabbing_v2.0.py
This commit is contained in:
Auden Cote-L'Heureux
GitHub
parent
bc72d5fca0
commit
7ba0b238ca
@ -1,213 +0,0 @@
|
||||
#Intent: Select clades of interest from large trees using taxonomic specifications
|
||||
#Requirements: A folder of trees and corresponding unaligned .fasta files
|
||||
#Example script call: python CladeGrabbing_v2.0.py --input /Path/to/trees --target Sr_rh --min_presence 20
|
||||
#For more info: python CladeGrabbing_v2.0.py --help
|
||||
|
||||
#Dependencies
|
||||
import os, re, sys
|
||||
from Bio import SeqIO
|
||||
import ete3
|
||||
import argparse
|
||||
|
||||
|
||||
def get_args():
|
||||
|
||||
parser = argparse.ArgumentParser(
|
||||
prog = 'Clade grabber, Version 2.0',
|
||||
description = "Updated March 26th, 2023 by Auden Cote-L'Heureux"
|
||||
)
|
||||
|
||||
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)')
|
||||
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.')
|
||||
parser.add_argument('-m', '--min_presence', type = int, required = True, help = 'Minimum number of target taxa present in clade for it to be selected')
|
||||
parser.add_argument('-a', '--at_least', 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).')
|
||||
parser.add_argument('-na', '--n_at_least', type = int, default = 0, help = 'The number of species belonging to taxa in the --at_least list that must be present in the clade. Default is 1.')
|
||||
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).')
|
||||
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.')
|
||||
|
||||
return parser.parse_args()
|
||||
|
||||
|
||||
def get_newick(fname):
|
||||
|
||||
newick = ''
|
||||
for line in open(fname):
|
||||
line = line.split(' ')[-1]
|
||||
if(line.startswith('(') or line.startswith('tree1=')):
|
||||
newick = line.split('tree1=')[-1].replace("'", '').replace('\\', '')
|
||||
|
||||
return newick
|
||||
|
||||
|
||||
#This function reroots the tree on the largest Ba/Za clade. If there is no prokaryote clade,
|
||||
#it roots on the largest Op clade, then Pl, then Am, then Ex, then Sr.
|
||||
def reroot(tree):
|
||||
|
||||
#This nested function returns the largest clade of a given taxonomic group
|
||||
def get_best_clade(taxon):
|
||||
|
||||
best_size = 0; best_clade = []; seen_leaves = []
|
||||
#Traverse all nodes
|
||||
for node in tree.traverse('levelorder'):
|
||||
#If the node is big enough and not subsumed by a node we've already accepted
|
||||
if len(node) >= 3 and len(list(set(seen_leaves) & set([leaf.name for leaf in node]))) == 0:
|
||||
leaves = [leaf.name for leaf in node]
|
||||
|
||||
#Create a record of leaves that belong to the taxonomic group
|
||||
target_leaves = set()
|
||||
for leaf in leaves[::-1]:
|
||||
if leaf[:2] in taxon:
|
||||
target_leaves.add(leaf[:10])
|
||||
leaves.remove(leaf)
|
||||
|
||||
#If this clade is better than any clade we've seen before, grab it
|
||||
if len(target_leaves) > best_size and len(leaves) <= 2:
|
||||
best_clade = node
|
||||
best_size = len(target_leaves)
|
||||
seen_leaves.extend([leaf.name for leaf in node])
|
||||
|
||||
return best_clade
|
||||
|
||||
#Get the biggest clade for each taxonomic group (stops once it finds one)
|
||||
for taxon in [('Ba', 'Za'), ('Op'), ('Pl'), ('Am'), ('Ex'), ('Sr')]:
|
||||
clade = get_best_clade(taxon)
|
||||
if len([leaf for leaf in clade if leaf.name[:2] in taxon]) > 3:
|
||||
tree.set_outgroup( clade)
|
||||
|
||||
break
|
||||
|
||||
return tree
|
||||
|
||||
|
||||
def get_subtrees(args, file):
|
||||
|
||||
newick = get_newick(args.input + '/' + file)
|
||||
|
||||
tree = ete3.Tree(newick)
|
||||
tree = reroot(tree)
|
||||
|
||||
#Getting a clean list of all target taxa
|
||||
if '.' in args.target:
|
||||
try:
|
||||
target_codes = [l.strip() for l in args.target.open().readlines() if l.strip() != '']
|
||||
except AttributeError:
|
||||
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')
|
||||
else:
|
||||
target_codes = [code.strip() for code in args.target.split(',') if code.strip() != '']
|
||||
|
||||
#Getting a clean list of all "at least" taxa
|
||||
if '.' in args.at_least:
|
||||
try:
|
||||
at_least_codes = [l.strip() for l in args.at_least.open().readlines() if l.strip() != '']
|
||||
except AttributeError:
|
||||
print('\n\nError: invalid "at_least" 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:
|
||||
at_least_codes = [code.strip() for code in args.at_least.split(',') if code.strip() != '']
|
||||
|
||||
target_codes = list(dict.fromkeys(target_codes + at_least_codes))
|
||||
|
||||
#Creating a record of selected subtrees, and all of the leaves in those subtrees
|
||||
selected_nodes = []; seen_leaves = []
|
||||
|
||||
#Iterating through all nodes in tree, starting at "root" then working towards leaves
|
||||
for node in tree.traverse('levelorder'):
|
||||
#If a node is large enough and is not contained in an already selected clade
|
||||
if len(node) >= args.min_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
|
||||
children_keep = 0
|
||||
for child in node.children:
|
||||
for code in target_codes:
|
||||
for leaf in child:
|
||||
if leaf.name.startswith(code):
|
||||
children_keep += 1
|
||||
break
|
||||
|
||||
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:
|
||||
at_least_leaves.add(leaf[:10])
|
||||
|
||||
leaves.remove(leaf)
|
||||
|
||||
#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
|
||||
if len(target_leaves) >= args.min_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
|
||||
for i, node in enumerate(selected_nodes[::-1]):
|
||||
with open('Subtrees/' + '.'.join(file.split('.')[:-1]) + '_' + str(i) + '.tre', 'w') as o:
|
||||
o.write(node.write())
|
||||
|
||||
|
||||
def make_new_unaligned(args):
|
||||
|
||||
if not os.path.isdir('Subtrees_unaligned'):
|
||||
os.mkdir('Subtrees_unaligned')
|
||||
|
||||
#Getting a clean list of outgroup taxa
|
||||
if '.' in args.outgroup:
|
||||
try:
|
||||
outgroup_codes = [l.strip() for l in args.outgroup.open().readlines() if l.strip() != '']
|
||||
except AttributeError:
|
||||
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')
|
||||
else:
|
||||
outgroup_codes = [code.strip() for code in args.outgroup.split(',') if code.strip() != '']
|
||||
|
||||
for tree_file in os.listdir('Subtrees'):
|
||||
if tree_file.endswith('.tre'):
|
||||
og = tree_file[:10]
|
||||
|
||||
tree = ete3.Tree('Subtrees/' + tree_file)
|
||||
|
||||
#Get the fasta (aligned or unaligned, but if aligned not columns removed) for each subtree
|
||||
for f, file in enumerate(os.listdir(args.input)):
|
||||
if file.startswith(og) and file.split('.')[-1] in ('fa', 'faa', 'fna', 'fasta', 'fas'):
|
||||
with open('Subtrees_unaligned/' + tree_file.replace('.tre', '.fasta'), 'w') as o:
|
||||
#For all records in the fasta file
|
||||
for rec in SeqIO.parse(args.input + '/' + file, 'fasta'):
|
||||
keep = False
|
||||
#Keep it if it's in the outgroup taxa list
|
||||
for code in outgroup_codes:
|
||||
if rec.id.startswith(code):
|
||||
keep = True
|
||||
break
|
||||
|
||||
#Or keep it if it's in the subtree
|
||||
if rec.description in [leaf.name for leaf in tree]:
|
||||
keep = True
|
||||
|
||||
#Write the sequence to the output file if kept
|
||||
if keep:
|
||||
o.write('>' + rec.description + '\n' + str(rec.seq).replace('-', '') + '\n\n')
|
||||
break
|
||||
|
||||
def main():
|
||||
|
||||
args = get_args()
|
||||
|
||||
if(not os.path.isdir('Subtrees')):
|
||||
os.mkdir('Subtrees')
|
||||
|
||||
f = 0
|
||||
for file in os.listdir(args.input):
|
||||
if file.split('.')[-1] in ('tre', 'tree', 'treefile', 'nex'):
|
||||
print(str(f + 1) + '. ' + file)
|
||||
f += 1
|
||||
|
||||
get_subtrees(args, file)
|
||||
|
||||
make_new_unaligned(args)
|
||||
|
||||
|
||||
main()
|
||||
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user