#!/usr/bin/env python3

# Script by Jason Kwong & Torsten Seemann

# Script to mask recombination from CFML output and draw SVG of recombinant regions

# Usage

import argparse

from argparse import RawTextHelpFormatter

parser = argparse.ArgumentParser(

formatter_class=RawTextHelpFormatter,

description='Mask recombination from ClonalFrameML/Gubbins output and draw SVG of recombinant regions',

usage='\n %(prog)s --aln FASTA --out OUTFILE [--gubbins] <PREFIX>')

parser.add_argument('prefix', metavar='PREFIX', help='prefix used for CFML/Gubbins input files (required)')

parser.add_argument('--gubbins', action='store_true', help='parse as Gubbins instead of ClonalFrameML')

parser.add_argument('--aln', metavar='FASTA', required=True, help='multiFASTA alignment used as input for CFML (required)')

parser.add_argument('--out', metavar='OUTFILE', default='maskrc.aln', help='output file for masked alignment (default="maskrc.aln")')

parser.add_argument('--symbol', metavar='CHAR', default='?', help='symbol to use for masking (default="?")')

parser.add_argument('--regions', metavar='FILE', help='output recombinant regions to file')

parser.add_argument('--svg', metavar='FILE', help='draw SVG output of recombinant regions and save as specified file'),

parser.add_argument('--svgsingle', action='store_true', help = 'draw a single SVG for each isolate in input, with isolate label as filename'),

parser.add_argument('--svgsize', metavar='WIDExHIGH', default='800x600', help='specify width and height of SVG in pixels (default="800x600")')

parser.add_argument('--svgorder', metavar='FILE', help='specify file containing list of taxa (1 per line) in desired order')

parser.add_argument('--svgcolour', metavar='COLOUR', default='black', help='specify colour of recombination regions in HEX format (default=black)')

parser.add_argument('--consensus', action='store_true', help='add consensus row of recombination hotspots')

parser.add_argument('--version', action='version', version='%(prog)s 0.5')

args = parser.parse_args()

prefix = str(args.prefix)

treefn = prefix + ('.labelled_tree.newick', '.final_tree.tre')[args.gubbins]

coordfn = prefix + ('.importation_status.txt', '.recombination_predictions.gff')[args.gubbins]

import os

import sys

import csv

from collections import defaultdict

from ete3 import Tree

from Bio import SeqIO

from Bio.Seq import Seq

from Bio.Seq import MutableSeq

from Bio.SeqRecord import SeqRecord

import svgwrite

from BCBio import GFF

import pprint

# Functions

def msg(*args, **kwargs):

print(*args, file=sys.stderr, **kwargs)

def err(*args, **kwargs):

msg(*args, **kwargs)

sys.exit(1);

def check_file(f):

msg('Checking file: {}'.format(f))

if os.path.isfile(f) == False:

err('ERROR: Cannot find "{}". Check output files exist in this directory.'.format(f))

# Check input files (output from CFML)

check_file(treefn)

check_file(coordfn)

# Setup lists and dictionary

d = defaultdict(list)

seqLIST = []

leafLIST = []

t = Tree(treefn, format=1)

# Set taxa order for SVG

if args.svgorder:

msg('Setting taxa order using --svgorder {}'.format(args.svgorder));

with open(args.svgorder) as file:

for row in file:

leafLIST.append(row.rstrip())

else:

msg('Setting taxa order using leaves from: {}'.format(treefn));

for leaf in t:

leafLIST.append(leaf.name)

# gubbins GFF

# node="internal_13->2016-04538";neg_log_likelihood="3764.359443";taxa="2016-04538";snp_count="108";

# node="internal_ROOT->internal_10";neg_log_likelihood="47939.649932";taxa=" 2016-23066 2015-19014";snp_count="8";

# node="internal_15->internal_16";neg_log_likelihood="574.375212";taxa=" 2008-16004 2010-22387";snp_count="39";

# node="internal_15->internal_16";neg_log_likelihood="418.840895";taxa=" 2008-16004 2010-22387";snp_count="38";

# node="internal_12->internal_14";neg_log_likelihood="17258.115166";taxa=" 2012-21203 2008-20031 2008-16004 2010-22387";

# clonalframeml "BED"

#Node Beg End

#2016-11776 5624 6619

#2016-11776 10778 11326

#Reference 2489729 2490893

#NODE_10 1165936 1166465

# internal

# ['Reference', ['2434777', '2434933', 'ancestral']],

# ['2016-17702', ['2483546', '2485711', 'ancestral']],

# ['2016-17705', ['2483546', '2485711', 'ancestral']],

# ['2016-11776', ['2483546', '2485711', 'ancestral']],

# ['2016-11778', ['2483546', '2485711', 'ancestral']],

# ['2016-11777', ['2483546', '2485711', 'ancestral']],

# ['2016-17701', ['2483546', '2485711', 'ancestral']],

# ['Reference', ['2483546', '2485711', 'ancestral']]]

if args.gubbins:

msg('Parsing Gubbins file: {}'.format(coordfn))

with open(coordfn) as gff:

for rec in GFF.parse(gff):

for f in rec.features:

taxa = f.qualifiers['taxa'][0].strip().split()

state = ('ancestral', 'extant')[ len(taxa)==1 ]

for taxon in taxa:

# BCBio-GFF module parser seems to extract coordinate-1 for f.location.start

seqLIST.append( [ taxon, [ int(f.location.start)+1, int(f.location.end), state ] ] )

else:

msg('Parsing ClonalFrameML file: {}'.format(coordfn))

with open(coordfn) as csvfile:

RCseqs = csv.reader(csvfile, delimiter='\t')

next(csvfile)

for row in RCseqs:

seq = row[0]

RCstart = row[1]

RCstop = row[2]

node = t.search_nodes(name=seq)[0]

if node.is_leaf():

leaf_names = [node.name]

z = 'extant'

else:

leaves = node.get_leaves()

leaf_names = [leaf.name for leaf in leaves]

z = 'ancestral'

for l in leaf_names:

seqLIST.append([l, [RCstart, RCstop, z]])

# Build dictionary of recombinant regions

for k,v in seqLIST:

d[k].append(v)

# Mask recombination in sequences

seqALN = []

for record in SeqIO.parse(args.aln, 'fasta'):

msg('Reading {} ... '.format(record.id))

seqlen = len(record.seq)

regions = d.get(record.id, None)

newrec = MutableSeq(str(record.seq))

if regions:

for a in regions:

start = int(a[0]) - 1

end = int(a[1])

lenMASK = end - start

newrec[start:end] = (args.symbol)*lenMASK

seqALN.append(SeqRecord(Seq(str(newrec)), record.id, description=''))

# Write masked alignment to file

msg('Writing masked alignment to {} ... '.format(args.out))

SeqIO.write(seqALN, args.out, 'fasta')

# Write recombinant regions to file

if args.regions:

with open(args.regions, 'w') as csvfile:

csvwriter = csv.writer(csvfile, delimiter='\t')

for k,v in list(d.items()):

for b in v:

x = b[0]

y = b[1]

z = b[2]

csvwriter.writerow([k,x,y,z])

# Draw SVG

svgsize = args.svgsize.split('x',1)

width = int(svgsize[0])

height = int(svgsize[1])

numseqs = len(leafLIST)

h = height/float(numseqs)

s = width/float(int(seqlen))

fsize = int(h*0.9)

font = 'font-size:{}px; font-family:Arial'.format(fsize)

colour = args.svgcolour

main_colour = 'black'

ancestral_colour = '#A9A9A9'

interval = 500000 # Tick interval in bp

# dwg = svgwrite.Drawing(args.svg)

def rect(x,p,w,colour, dwg): # Draw regions

dwg.add(dwg.rect(insert=((x*s)+5, (p*h)+5), size=(w, h*0.8), fill=colour))

if args.consensus:

dwg.add(dwg.rect(insert=((x*s)+5, 5), size=(w, h*0.8), fill=main_colour))

def label(n,p,dwg): # Sequence ID labels

dwg.add(dwg.text(n, insert=((seqlen*s)+15, (((p+1)*h)-(0.2*h))+5), fill=main_colour, style=font))

def ticks(q,dwg): # Draw tick marks

count = count + interval

def box(width,h,dwg): # Box with 5px margin

dwg.add(dwg.line((0,((p+1)*h)), (0,0), stroke=main_colour))

def positions(b,s):

return(x,y,z,w)

# Draw recombinant regions and labels

if args.svg or args.svgsingle:

msg('Drawing SVG to {} ...'.format(args.svg))

if args.consensus:

p = 1

dwg.add(dwg.text('Consensus', insert=((seqlen*s)+15, (0.8*h)+5), fill=main_colour, style=font))

else:

p = 0

if args.svg:

dwg = svgwrite.Drawing(args.svg)

for seq in leafLIST:

if args.svgsingle:

dwg = svgwrite.Drawing(f"{seq}.svg")

v = d.get(seq, None)

if v:

for b in v:

x,y,z,w = positions(b,s)

if w < 1:

w = 1

if z == 'extant':

rect(x,p,w,colour, dwg) # regions

elif z == 'ancestral':

rect(x,p,w,ancestral_colour, dwg)

label(seq,p, dwg) # labels

if args.svgsingle:

p = 0

dwg.save()

else:

p = p+1

if args.svg:

# Draw bounding box

box(width,h, dwg)

# Add tick marks

ticks(p+1, dwg)

dwg.save()

# Exit

msg('Done.')

sys.exit(0)