def fasta2vcf(fasta_file, outfile):
conf = get_conf_dict(sys.base_prefix + "/share/covidprofiler/%s" % args.db)
refseq = pp.fasta(conf["ref"]).fa_dict
seqs = pp.fasta(fasta_file)
samples = list(seqs.fa_dict.keys())
for sample in samples:
fname = pp.get_random_file()
open(fname, "w").write(">%s\n%s\n" % (sample, seqs.fa_dict[sample]))
fasta_obj = pp.fasta(fname)
vcf_obj = pp.vcf(fasta_obj.get_ref_variants(conf["ref"], sample))
pp.run_cmd("rm %s" % fname)
sample_chunks = [samples[i:i + 200] for i in range(0, len(samples), 200)]
tmp_vcfs = []
for tmp_samps in sample_chunks:
tmp_list = pp.get_random_file()
tmp_vcf = pp.get_random_file()
open(tmp_list,
"w").write("\n".join(["%s.vcf.gz" % x for x in tmp_samps]))
pp.run_cmd("bcftools merge -0 -l %s -Oz -o %s" % (tmp_list, tmp_vcf))
pp.run_cmd("bcftools index %s" % tmp_vcf)
tmp_vcfs.append(tmp_vcf)
pp.rm_files([tmp_list])
pp.run_cmd("bcftools merge -0 %s | bcftools view -V indels -Oz -o %s" %
(" ".join(tmp_vcfs), outfile))
vcf_files = ["%s.vcf.gz" % s for s in samples]
vcf_csi_files = ["%s.vcf.gz.csi" % s for s in samples]
pp.rm_files(vcf_files + vcf_csi_files + tmp_vcfs)
def main(args):
refseq = list(pp.fasta(args.ref).fa_dict.values())[0]
for l in sys.stdin:
if l[0] == "#":
if l.strip() == "##contig=<ID=1,length=29903>":
l = l.replace("1", "NC_045512.2")
sys.stdout.write(l)
continue
row = l.strip().split()
if row[0] == "1": row[0] = args.seqname
ipos = int(row[1]) - 1
possible_ref_allele = row[3]
true_ref_allele = refseq[ipos]
alts = row[4].split(",")
alleles = [possible_ref_allele] + alts
if possible_ref_allele != true_ref_allele:
ref_allele_index = alts.index(true_ref_allele)
row[3] = true_ref_allele
alts[ref_allele_index] = possible_ref_allele
row[4] = ",".join(alts)
genos = "".join(row[9:]).replace(
str(ref_allele_index + 1),
"R").replace("0", str(ref_allele_index + 1)).replace("R", "0")
row[9:] = list(genos)
sys.stdout.write("\t".join(row) + "\n")
else:
sys.stdout.write("\t".join(row) + "\n")
def main(args):
ref = pp.fasta(args.ref).fa_dict
cds = gff_load_cds(args.gff)
final_list = []
coding = defaultdict(list)
generator = pp.cmd_out(
f"bcftools view {args.vcf}") if args.vcf else sys.stdin
for l in generator:
row = l.strip().split()
if l[0] == "#":
sys.stdout.write(l.strip() + "\n")
elif len(row[3]) > 1 or len(row[4]) > 1:
final_list.append(row)
else:
gene, cpos = get_codon_pos(row[0], int(row[1]), cds)
if gene == None:
final_list.append(row)
else:
coding[(gene, cpos)].append(row)
for rows in coding.values():
chrom = rows[0][0]
pos = sorted([int(r[1]) for r in rows])
ref_nucs = {p: ref[chrom][p - 1] for p in range(pos[0], pos[-1] + 1)}
alt_nucs = ref_nucs.copy()
for i, p in enumerate(pos):
alt_nucs[p] = rows[i][4]
new_row = rows[0]
new_row[3] = "".join(ref_nucs.values())
new_row[4] = "".join(alt_nucs.values())
final_list.append(new_row)
for row in sorted(final_list, key=lambda x: int(x[1])):
sys.stdout.write("\t".join(row) + "\n")
def main(args):
seqs = pp.fasta(args.fasta).fa_dict
for seq in seqs:
seqs[seq] = list(seqs[seq])
for l in open(args.bed):
row = l.strip().split()
for i in tqdm(range(int(row[1])-1,int(row[2]))):
for seq in seqs:
seqs[seq][i] = "N"
with open(args.out,"w") as O:
for seq in seqs:
O.write(">%s\n%s\n" % (seq,"".join(seqs[seq])))
def main(args):
acgtn = set(["A","C","G","T","N"])
sys.stderr.write("Loading sequences\n")
seqs = pp.fasta(args.fasta).fa_dict
sys.stderr.write("Masking sequences\n")
for seq in tqdm(seqs):
nucs = Counter(list(seqs[seq]))
for nuc in nucs:
if nuc not in acgtn:
seqs[seq] = seqs[seq].replace(nuc,"N")
sys.stderr.write("Writing sequences\n")
with open(args.out,"w") as O:
for seq in seqs:
O.write(">%s\n%s\n" % (seq,"".join(seqs[seq])))
def main(args):
seqs = pp.fasta(args.msa).fa_dict
ref_pos = 0
print("ref_pos\talignment_pos\tA\tC\tG\tT\tN\tgap")
for i in range(len(list(seqs.values())[0])):
alignment_pos = i+1
if seqs[refseq][i]!="-":
ref_pos+=1
allele_count = Counter([seqs[s][i].upper() for s in seqs])
num_N = allele_count["N"] if "N" in allele_count else 0
num_gap = allele_count["-"] if "-" in allele_count else 0
num_A = allele_count["A"] if "A" in allele_count else 0
num_C = allele_count["C"] if "C" in allele_count else 0
num_G = allele_count["G"] if "G" in allele_count else 0
num_T = allele_count["T"] if "T" in allele_count else 0
print("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (ref_pos,alignment_pos,num_A,num_C,num_G,num_T,num_N,num_gap))
def primer_evaluation(args):
conf = get_conf_dict(sys.base_prefix + "/share/covidprofiler/%s" % args.db)
msa_obj = pp.fasta(conf["msa"]).fa_dict
forward_results = cp.run_fuzznuc(conf["msa"],
args.primerF,
pmismatch=args.mismatch)
reverse_results = cp.run_fuzznuc(conf["msa"],
args.primerR,
pmismatch=args.mismatch)
probe_results = cp.run_fuzznuc(conf["msa"],
args.probe,
pmismatch=args.mismatch)
rows = []
for s in tqdm(msa_obj):
amplicon = cp.find_amplicon(forward_results[s], reverse_results[s],
probe_results[s])
rows.append(amplicon)
with open(args.out, "w") as O:
writer = csv.DictWriter(O, fieldnames=list(rows[0].keys()))
writer.writeheader()
writer.writerows(rows)
def main(args):
conf = get_conf_dict(sys.base_prefix + "/share/tbprofiler/%s" % args.db)
if args.samples:
samples = [x.rstrip() for x in open(args.samples).readlines()]
else:
samples = [
x.replace(".targets.csq.vcf.gz", "") for x in os.listdir(args.dir)
if x[-19:] == ".targets.csq.vcf.gz"
]
sample_fastas = defaultdict(list)
params = {
"tmp_locations": pp.get_random_file(),
"tmp_mappings": pp.get_random_file(),
"ref": conf["ref"]
}
pp.run_cmd("awk '{print $1\":\"$2\"-\"$3\"\\t\"$5}' %s > %s" %
(conf["bed"], params["tmp_mappings"]))
pp.run_cmd("cut -f1 %s > %s" %
(params["tmp_mappings"], params["tmp_locations"]))
FILES = {}
for l in open(params["tmp_mappings"]):
row = l.rstrip().split()
FILES[row[0]] = open("%s.fasta" % row[1], "w")
for s in samples:
params["vcf"] = "%s/%s.targets.csq.vcf.gz" % (args.dir, s)
params["tmp_vcf"] = "%s/%s.targets.csq.tmp.vcf.gz" % (args.dir, s)
params["sample_fa"] = "%s.targets.fa" % (s)
pp.run_cmd(
"bcftools filter -e 'sum(AD)=0' -S . %(vcf)s | bcftools view -a | grep -v NON_REF | bcftools view -Oz -o %(tmp_vcf)s"
% params)
pp.run_cmd("bcftools index %(tmp_vcf)s" % params)
pp.run_cmd(
"samtools faidx -r %(tmp_locations)s %(ref)s | bcftools consensus -H A %(tmp_vcf)s > %(sample_fa)s"
% params)
fa_dict = pp.fasta(params["sample_fa"]).fa_dict
for locus in fa_dict:
FILES[locus].write(">%s\n%s\n" % (s, fa_dict[locus]))
pp.rm_files([params["tmp_vcf"]])
pp.rm_files([params["tmp_locations"], params["tmp_mappings"]])
def main(args):
genes = load_gff(args.gff)
refseq = pp.fasta(args.ref).fa_dict
mutations = {}
converted_mutations = {}
for row in csv.DictReader(open(args.csv)):
gene = [
g for g in genes
if g.name == row["Gene"] or g.locus_tag == row["Gene"]
][0]
mut = None
r = re.search("r.([0-9]+)([acgt]+)>([acgt]+)", row["Mutation"])
if r:
converted_mutations[(
row["Gene"], row["Mutation"]
)] = f"n.{r.group(1)}{r.group(2).upper()}>{r.group(3).upper()}"
r = re.search("p\..+", row["Mutation"])
if r:
converted_mutations[(row["Gene"],
row["Mutation"])] = row["Mutation"]
r = re.search("c.-[0-9]+[ACGT]>[ACGT]", row["Mutation"])
if r:
converted_mutations[(row["Gene"],
row["Mutation"])] = row["Mutation"]
r = re.search("c.[0-9]+dup[ACGT]+", row["Mutation"])
if r:
converted_mutations[(row["Gene"],
row["Mutation"])] = row["Mutation"]
r = re.search("c.[0-9]+_[0-9]+dup[ACGT]+", row["Mutation"])
if r:
converted_mutations[(row["Gene"],
row["Mutation"])] = row["Mutation"]
r = re.search("c.([0-9]+)del", row["Mutation"])
if r:
# "ethA" "c.341del"
del_start = int(r.group(1))
del_end = int(r.group(1))
if gene.strand == "+":
# rpoB "c.1282_1290del"
genome_start = gene.start + del_start - 2
genome_end = gene.start + del_end
else:
# "ethA" "c.1057_1059del"
genome_start = gene.start - del_end
genome_end = gene.start - del_start + 2
ref = refseq["Chromosome"][genome_start - 1:genome_end - 1]
alt = ref[0]
mutations[(row["Gene"], row["Mutation"])] = {
"pos": genome_start,
"ref": ref,
"alt": alt,
"gene": row["Gene"],
"type": "nucleotide"
}
r = re.search("c.([0-9]+)_([0-9]+)del", row["Mutation"])
if r:
del_start = int(r.group(1))
del_end = int(r.group(2))
if gene.strand == "+":
# rpoB "c.1282_1290del"
genome_start = gene.start + del_start - 2
genome_end = gene.start + del_end
else:
# "ethA" "c.1057_1059del"
genome_start = gene.start - del_end
genome_end = gene.start - del_start + 2
ref = refseq["Chromosome"][genome_start - 1:genome_end - 1]
alt = ref[0]
mutations[(row["Gene"], row["Mutation"])] = {
"pos": genome_start,
"ref": ref,
"alt": alt,
"gene": row["Gene"],
"type": "nucleotide"
}
r = re.search("c.-([0-9]+)del", row["Mutation"])
if r:
del_start = int(r.group(1))
del_end = int(r.group(1))
if gene.strand == "+":
# "embA" "c.-29_-28del"
genome_start = gene.start + del_start - 1
genome_end = gene.start + del_end + 1
else:
# "alr" "c.-283_-280delCAAT"
genome_start = gene.start - del_end - 1
genome_end = gene.start - del_start + 1
ref = refseq["Chromosome"][genome_start - 1:genome_end - 1]
alt = ref[0]
mutations[(row["Gene"], row["Mutation"])] = {
"pos": genome_start,
"ref": ref,
"alt": alt,
"gene": row["Gene"],
"type": "nucleotide"
}
r = re.search("c.(-[0-9]+)_(-[0-9]+)del", row["Mutation"])
if r:
del_start = int(r.group(1))
del_end = int(r.group(2))
if gene.strand == "+":
# "embA" "c.-29_-28del"
genome_start = gene.start + del_start - 1
genome_end = gene.start + del_end + 1
else:
# "alr" "c.-283_-280delCAAT"
genome_start = gene.start - del_end - 1
genome_end = gene.start - del_start + 1
ref = refseq["Chromosome"][genome_start - 1:genome_end - 1]
alt = ref[0]
mutations[(row["Gene"], row["Mutation"])] = {
"pos": genome_start,
"ref": ref,
"alt": alt,
"gene": row["Gene"],
"type": "nucleotide"
}
r = re.search("c.([0-9]+)_([0-9]+)ins([ACGT]+)", row["Mutation"])
if r:
ins_start = int(r.group(1))
ins_end = int(r.group(2))
ins_seq = r.group(3)
if gene.strand == "+":
# "rpoB" "c.1296_1297insTTC"
genome_start = gene.start + ins_start - 1
genome_end = gene.start + ins_end - 1
else:
# "pncA" "c.521_522insT"
ins_seq = pp.revcom(ins_seq)
genome_start = gene.start - ins_start
genome_end = gene.start - ins_end + 2
ref = refseq["Chromosome"][genome_start - 1:genome_end - 1]
alt = ref + ins_seq
mutations[(row["Gene"], row["Mutation"])] = {
"pos": genome_start,
"ref": ref,
"alt": alt,
"gene": row["Gene"],
"type": "nucleotide"
}
if row["Mutation"] == "frameshift":
converted_mutations[(row["Gene"],
row["Mutation"])] = row["Mutation"]
if row["Mutation"] == "large_deletion":
converted_mutations[(row["Gene"],
row["Mutation"])] = row["Mutation"]
if row["Mutation"][:19] == "any_missense_codon_":
converted_mutations[(row["Gene"],
row["Mutation"])] = row["Mutation"]
print("Converting %s mutations" % len(mutations))
mutation_conversion = get_ann(mutations)
for key in mutation_conversion:
converted_mutations[key] = mutation_conversion[key]
with open(args.out + ".csv", "w") as O:
with open(args.out + ".log", "w") as L:
writer = csv.DictWriter(O, fieldnames=list(row))
writer.writeheader()
for row in csv.DictReader(open(args.csv)):
key = (row["Gene"], row["Mutation"])
if row["Mutation"] != converted_mutations[key]:
L.write(
f'Recoded {row["Gene"]} {row["Mutation"]} as {converted_mutations[key]}\n'
)
row["Mutation"] = converted_mutations[key]
writer.writerow(row)
def main(args):
vcf_class = pp.vcf(args.vcf)
vcf_positions = vcf_class.get_positions()
if not args.fasta:
if not args.ref:
sys.stderr.write(
"\nERROR: Please supply a reference with --ref\n\n")
quit()
pp.run_cmd(
"vcf2fasta.py --vcf %(vcf)s --snps --ref %(ref)s --snps-no-filt" %
vars(args))
args.fasta = "%s.snps.fa" % vcf_class.prefix
if pp.nofile("%s.asr.state" % args.fasta):
pp.run_cmd(
"iqtree -m %(model)s -te %(tree)s -s %(fasta)s -nt AUTO -asr -pre %(fasta)s.asr"
% vars(args))
tree = ete3.Tree("%s.asr.treefile" % args.fasta, format=1)
node_names = set([tree.name] +
[n.name.split("/")[0] for n in tree.get_descendants()])
leaf_names = set(tree.get_leaf_names())
internal_node_names = node_names - leaf_names
states_file = "%s.asr.state" % args.fasta
states = defaultdict(dict)
sys.stderr.write("Loading states\n")
for l in tqdm(open(states_file)):
if l[0] == "#": continue
row = l.strip().split()
if row[0] == "Node": continue
site = int(row[1])
if row[0] not in internal_node_names: continue
states[site][row[0]] = row[2]
seqs = pp.fasta(args.fasta).fa_dict
for site in tqdm(list(states)):
for sample in seqs:
states[site][sample] = seqs[sample][site - 1]
acgt = set(["A", "C", "G", "T", "a", "c", "g", "t"])
convergent_sites = []
for site in tqdm(list(states)):
nucleotides = set([states[site][n] for n in node_names])
if len(nucleotides) == 1: continue
# Set up storage objects
origins = []
tree.add_feature("state", states[site][tree.name])
for n in tree.traverse():
if n == tree: continue
node_state = states[site][n.name]
if node_state != n.get_ancestors(
)[0].state and node_state in acgt and n.get_ancestors(
)[0].state in acgt:
origins.append(n.name)
n.add_feature("state", node_state)
if len(origins) > 1:
convergent_sites.append((site, vcf_positions[site - 1], origins))
with open(args.out, "w") as O:
for site in convergent_sites:
O.write("%s\t%s\n" % (site[1][1], len(site[2])))
def main_preprocess(args):
conf = get_conf_dict(sys.base_prefix + "/share/covidprofiler/%s" % args.db)
refseq = pp.fasta(conf["ref"]).fa_dict
refseqname = list(refseq.keys())[0]
if args.seqs:
seqs = pp.fasta(args.seqs)
samples = list(seqs.fa_dict.keys())
fasta2vcf(args.seqs, "merged.vcf.gz")
#
#
# pp.run_cmd("vcf2fasta.py --vcf merged.vcf.gz --ref %s" % conf["ref"])
# pp.run_cmd("iqtree -s merged.fa -m GTR+F+R2 -bb 1000 -nt AUTO -asr -czb -redo")
variant_data = get_variant_data("merged.vcf.gz", conf["ref"], conf["gff"],
conf["proteins"])
#### variant_data = {29366: {'alts': 'T', 'types': 'missense', 'changes': '365P>365S', 'gene': 'N', 'gene_function': 'Nucleocapsid protein', 'gene_reference': '10.1186/s40779-020-00240-0'}}
#### mutations = [{'position': 29868, 'mutation_type': 'convergent', 'origins': 14, 'branches': 'Node927'}]
for i in range(len(mutations)):
for key in variant_data[mutations[i]["position"]]:
mutations[i][key] = variant_data[mutations[i]["position"]][key]
with open(args.out + ".csv", "w") as O:
tmp = list(mutations[0].keys())
fieldnames = tmp[:4] + tmp[-6:] + tmp[4:-6]
writer = csv.DictWriter(O, fieldnames=fieldnames)
writer.writeheader()
writer.writerows(mutations)
quit()
seqs = pp.fasta("merged.fa").fa_dict
tree = ete3.Tree("merged.fa.treefile", format=1)
node_names = set([tree.name] +
[n.name.split("/")[0] for n in tree.get_descendants()])
leaf_names = set(tree.get_leaf_names())
internal_node_names = node_names - leaf_names
for n in tree.traverse():
if n.name.split("/")[0] in node_names:
if "Node" in n.name:
tmp = n.name.split("/")
n.name = tmp[0]
if len(tmp) > 1:
n.support = tmp[1]
states = defaultdict(dict)
sites = set()
sys.stderr.write("Loading states\n")
for l in tqdm(open("merged.fa.state")):
if l[0] == "#": continue
row = l.strip().split()
if row[0] == "Node": continue
states[int(row[1])][row[0]] = row[2]
sites.add(int(row[1]))
sys.stderr.write("Loading alignment sites\n")
for site in tqdm(sites):
for sample in seqs:
states[site][sample] = seqs[sample][site - 1]
barcoding_sites = []
convergent_sites = []
mutations = []
for site in tqdm(sites):
if site not in variant_data:
continue ####### Not sure if this is right yet
nucleotides = set([states[site][n] for n in node_names])
if len(nucleotides) == 1: continue
# Set up storage objjects
origins = []
internal_node_change = False
tree.add_feature("state", states[site][tree.name])
for n in tree.traverse():
if n == tree: continue
node_state = states[site][n.name]
if node_state != n.get_ancestors()[0].state:
origins.append(n.name)
if n.name in internal_node_names:
internal_node_change = True
n.add_feature("state", node_state)
type = "unique"
if internal_node_change and len(origins) == 1:
type = "barcoding"
barcoding_sites.append(site)
if len(origins) > 1:
type = "convergent"
convergent_sites.append(site)
tmp_data = {
"position": site,
"mutation_type": type,
"origins": len(origins),
"branches": ",".join(origins),
"gene": variant_data[site]["gene"],
"gene_function": variant_data[site]["gene_function"],
"gene_reference": variant_data[site]["gene_reference"],
"alts": variant_data[site]["alts"],
"functional_types": variant_data[site]["types"],
"changes": variant_data[site]["changes"]
}
for sample in leaf_names:
tmp_data[sample] = states[site][sample]
mutations.append(tmp_data)
print("Barcoding sites: ", barcoding_sites)
print("Convergent sites: ", convergent_sites)
# Reroot tree at S/L types
outgroup_leaf_names = [s for s in leaf_names if seqs[s][8782 - 1] == "T"]
tree.set_outgroup(tree.get_common_ancestor(outgroup_leaf_names))
tree.write(format=1, outfile=args.out + ".tree")
with open(args.out + ".barcode.bed", "w") as O:
for pos in barcoding_sites:
for allele in set(list(states[pos].values())):
tmp_samps = [x for x in leaf_names if states[pos][x] == allele]
O.write("%s\t%s\t%s\t%s\t%s\n" %
(refseqname, pos - 1, pos, allele,
tree.get_common_ancestor(tmp_samps).name))
with open(args.out + ".mutation_summary.csv", "w") as O:
writer = csv.DictWriter(
O,
fieldnames=[
"position", "mutation_type", "origins", "branches", "gene",
"gene_function", "gene_reference", "alts", "functional_types",
"changes"
] + list(leaf_names))
writer.writeheader()
for row in mutations:
writer.writerow(row)
def main_profile(args):
if pp.nofolder(args.dir):
os.mkdir(args.dir)
conf = get_conf_dict(sys.base_prefix + "/share/covidprofiler/%s" % args.db)
### Setup prefix for files ###
files_prefix = args.dir + "/" + args.prefix
if args.fasta:
if args.read1 or args.read2:
sys.stderr.write(
"Please use --fasta or --read1/2 but not both... Exiting!\n")
quit()
fasta_obj = pp.fasta(args.fasta)
wg_vcf_obj = pp.vcf(
fasta_obj.get_ref_variants(conf["ref"],
prefix=args.prefix,
file_prefix=files_prefix))
else:
if not args.read1:
sys.stderr.write(
"Please provide assembly using --fasta or at least one read file using --read1... Exiting!\n"
)
quit()
### Create bam file if fastq has been supplied ###
if args.read1 and args.read2 and args.no_trim:
# Paired + no trimming
fastq_obj = pp.fastq(args.read1, args.read2)
elif args.read1 and args.read2 and not args.no_trim:
# Paired + trimming
untrimmed_fastq_obj = pp.fastq(args.read1, args.read2)
fastq_obj = untrimmed_fastq_obj.trim(files_prefix,
threads=args.threads)
elif args.read1 and not args.read2 and args.no_trim:
# Unpaired + trimming
fastq_obj = pp.fastq(args.read1, args.read2)
elif args.read1 and not args.read2 and not args.no_trim:
# Unpaired + trimming
untrimmed_fastq_obj = pp.fastq(args.read1)
fastq_obj = untrimmed_fastq_obj.trim(files_prefix,
threads=args.threads)
bam_obj = fastq_obj.map_to_ref(ref_file=conf["ref"],
prefix=files_prefix,
sample_name=args.prefix,
aligner=args.mapper,
platform=args.platform,
threads=args.threads)
wg_vcf_obj = bam_obj.call_variants(conf["ref"],
args.caller,
remove_missing=True)
cp.vcf2consensus(bam_obj.bam_file, wg_vcf_obj.filename, conf["ref"],
wg_vcf_obj.samples[0],
wg_vcf_obj.prefix + ".consensus.fasta")
if not args.no_trim:
pp.run_cmd("rm -f %s" % " ".join(fastq_obj.files))
refseq = pp.fasta(conf["ref"]).fa_dict
refseqname = list(refseq.keys())[0]
results = {}
barcode_mutations = wg_vcf_obj.get_bed_gt(conf["barcode"], conf["ref"])
barcode = pp.barcode(barcode_mutations, conf["barcode"])
clade = ";".join(sorted([d["annotation"] for d in barcode]))
sys.stdout.write("%s\t%s\n" % (args.prefix, clade))
results["clade"] = clade
variant_data = cp.get_variant_data(wg_vcf_obj.filename, conf["ref"],
conf["gff"], conf["proteins"])
results["variants"] = variant_data
json.dump(results, open("%s.results.json" % files_prefix, "w"))
def main(args):
if args.bed:
pp.split_bed(args.bed, args.size, reformat=args.reformat)
else:
fasta = pp.fasta(args.fasta)
fasta.splitchr(args.size, reformat=args.reformat)
def find_ancestral_mutations(msa_file,
tree_file,
states_file,
variant_sites=None):
seqs = pp.fasta(msa_file).fa_dict
tree = ete3.Tree(tree_file, format=1)
node_names = set([tree.name] +
[n.name.split("/")[0] for n in tree.get_descendants()])
leaf_names = set(tree.get_leaf_names())
internal_node_names = node_names - leaf_names
for n in tree.traverse():
if n.name.split("/")[0] in node_names:
if "Node" in n.name:
tmp = n.name.split("/")
n.name = tmp[0]
if len(tmp) > 1:
n.support = tmp[1]
tree.write(format=1, outfile=tree_file + ".reformatted.tree")
states = defaultdict(dict)
sites = set()
sys.stderr.write("Loading states\n")
for l in tqdm(open(states_file)):
if l[0] == "#": continue
row = l.strip().split()
if row[0] == "Node": continue
site = int(row[1])
if variant_sites and site not in variant_sites: continue
if row[0] not in internal_node_names: continue
states[site][row[0]] = row[2]
sites.add(site)
sys.stderr.write("Loading alignment sites\n")
for site in tqdm(sites):
for sample in seqs:
states[site][sample] = seqs[sample][site - 1]
barcoding_sites = []
convergent_sites = []
mutations = []
for site in tqdm(sites):
nucleotides = set([states[site][n] for n in node_names])
if len(nucleotides) == 1: continue
# Set up storage objjects
origins = []
internal_node_change = False
tree.add_feature("state", states[site][tree.name])
for n in tree.traverse():
if n == tree: continue
node_state = states[site][n.name]
if node_state != n.get_ancestors(
)[0].state and node_state != "N" and n.get_ancestors(
)[0].state != "N":
origins.append(n.name)
if n.name in internal_node_names:
internal_node_change = True
n.add_feature("state", node_state)
type = "unique"
if internal_node_change and len(origins) == 1:
type = "barcoding"
barcoding_sites.append(site)
if len(origins) > 1:
type = "convergent"
convergent_sites.append(site)
tmp_data = {
"position": site,
"mutation_type": type,
"origins": len(origins),
"branches": ",".join(origins),
}
for sample in leaf_names:
tmp_data[sample] = states[site][sample]
mutations.append(tmp_data)
return mutations