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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_clade')
# input options
parser.add_argument('--list',
help = 'List of sequences to extract',
required = True)
parser.add_argument('--aln',
help = 'Input alignment (FASTA format)',
required = True)
parser.add_argument('--gff',
help = 'GFF of recombinant regions detected by Gubbins',
required = True)
parser.add_argument('--tree',
help = 'Final tree generated by Gubbins',
required = True)
parser.add_argument('--out',
help = 'Output file prefix',
required = True)
parser.add_argument('--out-fmt',
help = 'Format of output alignment',
default = 'fasta')
parser.add_argument('--missing-char',
help = 'Character used to replace recombinant sequence',
default = '-')
return parser.parse_args()
# main code
if __name__ == "__main__":
# Get command line options
args = get_options()
# Parse list of input sequences
subset = set()
# Read in FASTA assemblies
with open(args.list,'r') as seq_list:
for line in seq_list.readlines():
subset.add(line.strip().split()[0])
# Extract from alignment
output_aln_name = args.out + '.aln'
names_in_alignment = set()
sequences_to_print = []
alignment = AlignIO.read(args.aln,'fasta')
for taxon in alignment:
names_in_alignment.add(taxon.id)
if taxon.id in subset:
sequences_to_print.append(taxon)
# Check subset sequences are found in alignment
not_found_in_dataset = subset - names_in_alignment
if len(not_found_in_dataset) > 0:
sys.stderr.write('Sequences in subset missing from alignment: ' + \
str(not_found_in_dataset) + '\n')
sys.exit(1)
# Prune from the tree
output_tree_name = args.out + '.tree'
tree = dendropy.Tree.get(path = args.tree,
schema = 'newick',
preserve_underscores = True)
tree.retain_taxa_with_labels(subset)
tree.write_to_path(output_tree_name,
'newick')
# Identify relevant recombination blocks
recombination_starts = []
recombination_ends = []
recombination_taxa = []
output_gff_name = args.out + '.gff'
taxon_pattern = re.compile('taxa="([^"]*)"')
with open(args.gff,'r') as in_gff, open(output_gff_name,'w') as out_gff:
for line in in_gff.readlines():
if line.startswith('##'):
out_gff.write(line)
else:
info = line.rstrip().split('\t')
taxon_set = set(taxon_pattern.search(info[8]).group(1).split())
if not taxon_set.isdisjoint(subset):
out_gff.write(line)
if len(taxon_set) < len(subset):
recombination_starts.append(int(info[3]))
recombination_ends.append(int(info[4]))
recombination_taxa.append(frozenset(taxon_set))
# Write out masked alignment for clade
with open(output_aln_name,'w') as out_aln:
for taxon in sequences_to_print:
for index,taxa in enumerate(recombination_taxa):
if taxon.id in taxa:
seq_string = str(taxon.seq)
replacement_string = args.missing_char*(recombination_ends[index] - recombination_starts[index] + 1)
seq_string = seq_string[:recombination_starts[index]-1] + replacement_string + seq_string[recombination_ends[index]:]
taxon.seq = Seq(seq_string)
SeqIO.write(taxon, out_aln, args.out_fmt)
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