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257 lines
10 KiB
Python
257 lines
10 KiB
Python
import os, sys, re
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from Bio import SeqIO
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import ete3
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import guidance
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import trees
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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(file)
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tree = ete3.Tree(newick)
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try:
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tree = reroot(tree)
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except:
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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')
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#Getting a clean list of all target taxa
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if os.path.isfile(args.target):
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try:
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target_codes = [l.strip() for l in open(args.target).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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#make sure that this is how nargs works
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target_codes = [code.strip() for code in args.target if code.strip() != '']
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#Getting a clean list of all "at least" taxa
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if os.path.isfile(args.required_taxa):
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try:
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at_least_codes = [l.strip() for l in open(args.required_taxa).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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#make sure that this is how nargs works
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at_least_codes = [code.strip() for code in args.required_taxa if code.strip() != '']
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target_codes = list(dict.fromkeys(target_codes + at_least_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 a node is large enough and is not contained in an already selected clade
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if len(node) >= args.min_target_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 with 1 fewer than the max number of contaminants
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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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for leaf in child:
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if leaf.name.startswith(code):
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children_keep += 1
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break
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if children_keep == len(node.children):
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#Creating a record of all leaves belonging to the target/"at least" group of taxa, and any other leaves are contaminants
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target_leaves = set(); at_least_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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if code in at_least_codes:
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at_least_leaves.add(leaf[:10])
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leaves.remove(leaf)
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#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
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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):
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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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seqs2keep = [leaf.name for node in selected_nodes for leaf in node]
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return seqs2keep
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def get_sisters(args, file, contam_per_tax):
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seqs2remove = []
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#Read the tree using ete3 and reroot it using the above function
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newick = get_newick(file)
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tree = ete3.Tree(newick)
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try:
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tree = reroot(tree)
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except:
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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')
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#For each sequence
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for leaf in tree:
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#This loop will keep moving towards the root of the tree until it finds a node that
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#has leaves from a cell other than the one for which we are looking for sisters
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parent_node = leaf; sister_taxa = {leaf.name[:10]}
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while len(sister_taxa) == 1:
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parent_node = parent_node.up
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for l2 in parent_node:
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sister_taxa.add(l2.name[:10])
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#Create a record of the sister sequences
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sisters = list(dict.fromkeys([sister for sister in parent_node if sister.name[:10] != leaf.name[:10]]))
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bad_sisters = list(dict.fromkeys([contam for tax in contam_per_tax for contam in contam_per_tax[tax] if leaf.name.startswith[tax]]))
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sisters_removable = []
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for contam in bad_sisters:
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for sister in sisters:
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if sister.startswith(contam) and sister not in sisters_removable:
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sisters_removable.append(sister)
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if len(sisters_removable) == len(sisters):
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seqs2remove.append(leaf.name)
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return [leaf.name for leaf in tree if leaf.name not in seqs2remove]
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def write_new_preguidance(params, seqs2keep, seqs_per_og):
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prefix = '.'.join(tree_file.split('.')[:-1])
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seq_file = [file for file in seqs_per_og if file.startswith(prefix)]
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if len(seq_file) == 0:
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seq_file = [file for file in seqs_per_og if file.startswith(prefix.split('.')[0])]
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if len(seq_file) == 0:
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print('\nNo sequence file found for tree file ' + tree_file + '. Skipping this gene family.\n')
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elif len(seq_file) > 1:
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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')
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if len(seq_file) == 1:
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with open(params.output + '/Pre-Guidance/' + seq_file, 'w') as o:
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for rec in seqs_per_og[seq_file]:
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if rec in seqs2keep:
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o.write('>' + rec + '\n' + seqs_per_og[seq_file][rec] + '\n\n')
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na
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seqs_removed_from_og = [seq for seq in seqs_per_og[seq_file] if seq not in seqs2keep]
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def run(params):
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seqs_removed = []
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completed_ogs = []
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for loop in range(params.nloops):
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if params.start == 'raw':
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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') }
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elif params.start in ('unaligned', 'aligned', 'trees'):
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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') }
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if loop > 0 or params.start == 'raw':
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os.system('mv ' + params.output + '/Pre-Guidance ' + params.output + '/Pre-Guidance_' + str(loop))
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os.mkdir(params.output + '/Pre-Guidance')
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if params.contamination_loop == 'clade':
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for tree_file in params.output + '/Trees':
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if tree_file.split('.')[-1] in ('tre', 'tree', 'treefile', 'nex') and tree_file not in completed_ogs:
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seqs2keep = get_subtrees(params, params.output + '/Trees/' + tree_file)
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seqs_removed_from_og = write_new_preguidance(params, seqs2keep, seqs_per_og)
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if len(seqs_removed_from_og) == 0:
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completed_ogs.append(tree_file)
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else:
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seqs_removed += [seq for seq in seqs_per_og[seq_file] if seq not in seqs2keep]
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elif params.contamination_loop == 'seq':
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contam_per_tax = { line.strip().split('\t')[0] : line.strip().split('\t')[1:] for line in params.sister_rules }
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if params.contamination_loop == 'clade':
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for tree_file in params.output + '/Trees':
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if tree_file.split('.')[-1] in ('tre', 'tree', 'treefile', 'nex') and tree_file not in completed_ogs:
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seqs2keep = get_sisters(params, params.output + '/Trees/' + tree_file, contam_per_tax)
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seqs_removed_from_og = write_new_preguidance(params, seqs2keep, seqs_per_og)
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if len(seqs_removed_from_og) == 0:
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completed_ogs.append(tree_file)
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else:
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seqs_removed += [seq for seq in seqs_per_og[seq_file] if seq not in seqs2keep]
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os.system('mv ' + params.output + '/Trees ' + params.output + '/Trees_' + str(loop))
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os.mkdir(params.output + '/Trees')
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os.system('mv ' + params.output + '/Guidance ' + params.output + '/Guidance_' + str(loop))
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os.mkdir(params.output + '/Guidance')
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params.start = 'unaligned'
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params.end = 'trees'
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guidance.run(params)
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trees.run(params)
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with open('SequencesRemoved_ContaminationLoop.txt', 'w') as o:
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for seq in seqs_removed:
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o.write(seq + '\n')
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