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#! python
# encoding: utf-8
# Wellcome Trust Sanger Institute and Imperial College London
# Copyright (C) 2020 Wellcome Trust Sanger Institute and Imperial College London
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
#
# Generic imports
import sys
import argparse
import re
# Phylogenetic imports
import dendropy
# Biopython imports
from Bio import AlignIO
from Bio import Phylo
from Bio import SeqIO
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
# command line parsing
def get_options():
parser = argparse.ArgumentParser(description='Extract a clade from a Gubbins output',
prog='extract_gubbins_clade')
# input options
parser.add_argument('--clades',
help = 'Two column file assigning isolates (first column) to clades (second column)',
required = True)
parser.add_argument('--gff',
help = 'recombination prediction GFF file output by Gubbins',
required = True)
parser.add_argument('--snps',
help = 'branch base reconstruction EMBL file output by Gubbins',
required = True)
parser.add_argument('--exclude-regions',
help = 'Two column file specifying start and end of regions to be excluded',
required = False,
default = None)
parser.add_argument('--tree',
help = 'Labelled tree output by Gubbins',
required = True)
parser.add_argument('--print-trees',
help = 'Print clade trees',
default = False,
action = 'store_true')
parser.add_argument('--print-rec-lengths',
help = 'Print recombination lengths',
default = False,
action = 'store_true')
parser.add_argument('--out',
help = 'Output file prefix; suffix is "_clades.csv"',
required = True)
return parser.parse_args()
# main code
if __name__ == "__main__":
# Get command line options
args = get_options()
# Parse clades
clades = {}
clade_names = set()
with open(args.clades,'r') as clade_list:
for line in clade_list.readlines():
info = line.strip().split()
if len(info) == 2:
clades[info[0]] = info[1]
clade_names.add(info[1])
else:
sys.stderr.write('Line needs two columns: ' + line + '\n')
# Exclude regions
excluded_region_starts = []
excluded_region_ends = []
if args.exclude_regions is not None:
with open(args.exclude_regions,'r') as exclude_file:
for line in exclude_file.readlines():
coords = line.strip().split()
if int(coords[0]) < int(coords[1]):
excluded_region_starts.append(int(coords[0]))
excluded_region_ends.append(int(coords[1]))
else:
sys.stderr.write('Start of excluded region must be less than end\n')
sys.exit(1)
# Store SNP information
node_snps = {}
snp_total = 0
with open(args.snps,'r') as snp_file:
pos = 0
for line in snp_file.readlines():
info = line.strip().split()
if info[1] == 'variation':
pos = int(info[2])
if info[1].startswith('/node='):
node = info[1].replace('"','').split('->')
include_snp = True
for s,e in zip(excluded_region_starts,excluded_region_ends):
if pos >= s and pos <= e:
include_snp = False
break
if include_snp:
snp_total += 1
if node[1] in node_snps:
node_snps[node[1]].append(pos)
else:
node_snps[node[1]] = [pos]
# Store recombination information
node_rec_starts = {}
node_rec_ends = {}
with open(args.gff,'r') as gff_file:
for line in gff_file.readlines():
if not line.startswith('##'):
info = line.rstrip().split('\t')
start = int(info[3])
end = int(info[4])
node = info[8].split(';')[0].replace('"','').split('->')[1]
include_rec = True
for s,e in zip(excluded_region_starts,excluded_region_ends):
if start >= s and end <= e:
include_rec = False
if include_rec:
if node not in node_rec_starts:
node_rec_starts[node] = [start]
node_rec_ends[node] = [end]
else:
node_rec_starts[node].append(start)
node_rec_ends[node].append(end)
# Divide SNPs into recombinant and non-recombinant
rec_snps = {node:0 for node in node_snps}
pm_snps = {node:0 for node in node_snps}
for node in node_snps:
for p in node_snps[node]:
rec_snp = False
if node in node_rec_starts:
for s,e in zip(node_rec_starts[node],node_rec_ends[node]):
if p >= s and p <= e:
rec_snp = True
break
if rec_snp:
rec_snps[node] += 1
else:
pm_snps[node] += 1
# Parse tree
info_labels = ['total_snps','rec_snps','mutation_snps','recombinations']
tree_info_labels = ['n_taxa','n_branches','branch_length']
tree = dendropy.Tree.get(path = args.tree,
schema = 'newick',
preserve_underscores = True,
rooting='force-rooted')
taxon_names = [taxon.label for taxon in tree.taxon_namespace]
# Calculate statistics per clade
rec_length_string = ''
with open(args.out + '_clades.csv','w') as out_file:
out_file.write('Clade,')
out_file.write(','.join(info_labels + tree_info_labels))
out_file.write('\n')
for clade_name in clade_names:
out_file.write(clade_name + ',')
clade_members = [sequence for sequence in clades if clades[sequence] == clade_name]
# Check all isolates are in the tree
for isolate in clade_members:
if isolate not in taxon_names:
sys.stderr.write('Isolate ' + isolate + ' not in tree\n')
sys.stderr.write('Tree contains ' + ','.join(taxon_names) + '\n')
#exit(1)
# Extract clade tree
clade_tree = tree.clone(depth = 1)
clade_tree.retain_taxa_with_labels(clade_members)
# Print tree
if args.print_trees:
clade_tree_string = clade_tree.as_string(
schema='newick',
suppress_leaf_taxon_labels=False,
suppress_leaf_node_labels=True,
suppress_internal_taxon_labels=True,
suppress_internal_node_labels=True,
suppress_rooting=True,
suppress_edge_lengths=False,
unquoted_underscores=True,
preserve_spaces=False,
store_tree_weights=False,
suppress_annotations=True,
annotations_as_nhx=False,
suppress_item_comments=True,
node_label_element_separator=' '
)
with open(clade_name + '.tre','w') as tree_out:
tree_out.write(clade_tree_string.replace('\'', '') + '\n')
# Print statistics
clade_info = {label:0 for label in info_labels + tree_info_labels}
for node in clade_tree.preorder_node_iter():
if node != clade_tree.seed_node:
clade_info['n_branches'] += 1
clade_info['branch_length'] += node.edge_length
if node.is_leaf():
clade_info['n_taxa'] += 1
node_label_string = node.taxon.label
else:
node_label_string = node.label
if node_label_string in node_snps:
clade_info['total_snps'] += len(node_snps[node_label_string])
clade_info['rec_snps'] += rec_snps[node_label_string]
clade_info['mutation_snps'] += pm_snps[node_label_string]
if node_label_string in node_rec_starts:
clade_info['recombinations'] += len(node_rec_starts[node_label_string])
if args.print_rec_lengths:
for s,e in zip(node_rec_starts[node_label_string],node_rec_ends[node_label_string]):
rec_length_string += clade_name + ',' + str(1+e-s) + '\n'
out_file.write(','.join([str(clade_info[label]) for label in info_labels + tree_info_labels]))
out_file.write('\n')
if args.print_rec_lengths:
with open(args.out + '_rec_lengths.csv','w') as rec_out_file:
rec_out_file.write('Clade,Length\n' + rec_length_string)
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