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create_table.py
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create_table.py
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#!/usr/bin/env python3
import argparse
import os
import json
import sys
import csv
import re
def parse_args(args=None):
Description = "Create a table by parsing json output to extract N50, BUSCO, QV and COMPLETENESS stats."
parser = argparse.ArgumentParser(description=Description)
parser.add_argument("--genome", help="Input NCBI genome summary JSON file.", required=True)
parser.add_argument("--sequence", help="Input NCBI sequence summary JSON file.", required=True)
parser.add_argument("--busco", help="Input BUSCO short summary JSON file.")
parser.add_argument("--qv", nargs="*", help="Input QV TSV file from MERQURYFK.")
parser.add_argument("--completeness", nargs="*", help="Input COMPLETENESS stats TSV file from MERQURYFK.")
parser.add_argument("--hic", action="append", help="HiC sample ID used for contact maps.")
parser.add_argument("--flagstat", action="append", help="HiC flagstat file created by Samtools.")
parser.add_argument("--outcsv", help="Output CSV file.", required=True)
parser.add_argument("--version", action="version", version="%(prog)s 3.1")
return parser.parse_args(args)
def make_dir(path):
if len(path) > 0:
os.makedirs(path, exist_ok=True)
# check_samplesheet.py adds a suffix like "_T1", "_T2", etc, to the sample names
# We usually don't want it in the final output
def remove_sample_T_suffix(name):
return re.sub(r"_T\d+", "", name)
def ncbi_stats(genome_in, seq_in, writer):
with open(genome_in, "r") as fin1:
data = json.load(fin1)
with open(seq_in, "r") as fin2:
seq = json.load(fin2)
data = data["reports"][0]
info = data["assembly_info"]
attr = info["biosample"]["attributes"]
stats = data["assembly_stats"]
seq = seq["reports"]
writer.writerow(["##Assembly_Information"])
writer.writerow(["Accession", data["accession"]])
if "common_name" in data["organism"]:
writer.writerow(["Common_Name", data["organism"]["common_name"]])
writer.writerow(["Organism_Name", data["organism"]["organism_name"]])
writer.writerow(
[
"ToL_ID",
"".join(pairs["value"] for pairs in attr if pairs["name"] == "tolid"),
]
)
writer.writerow(["Taxon_ID", data["organism"]["tax_id"]])
writer.writerow(["Assembly_Name", info["assembly_name"]])
writer.writerow(["Assembly_Level", info["assembly_level"]])
writer.writerow(
[
"Life_Stage",
"".join(pairs["value"] for pairs in attr if pairs["name"] == "life_stage"),
]
)
writer.writerow(
[
"Tissue",
"".join(pairs["value"] for pairs in attr if pairs["name"] == "tissue"),
]
)
writer.writerow(["Sex", "".join(pairs["value"] for pairs in attr if pairs["name"] == "sex")])
writer.writerow(["##Assembly_Statistics"])
writer.writerow(["Total_Sequence", stats["total_sequence_length"]])
if "total_number_of_chromosomes" in stats:
writer.writerow(["Chromosomes", stats["total_number_of_chromosomes"]])
writer.writerow(["Scaffolds", stats["number_of_scaffolds"]])
writer.writerow(["Scaffold_N50", stats["scaffold_n50"]])
writer.writerow(["Contigs", stats["number_of_contigs"]])
writer.writerow(["Contig_N50", stats["contig_n50"]])
writer.writerow(["GC_Percent", stats["gc_percent"]])
chromosome_header = False
for mol in seq:
if "gc_percent" in mol and mol["assembly_unit"] != "non-nuclear":
if not chromosome_header:
writer.writerow(["##Chromosome", "Length", "GC_Percent"])
chromosome_header = True
writer.writerow(
[
mol["chr_name"],
round(mol["length"] / 1000000, 2),
mol["gc_percent"],
]
)
organelle_header = False
for mol in seq:
if "gc_percent" in mol and mol["assembly_unit"] == "non-nuclear":
if not organelle_header:
writer.writerow(["##Organelle", "Length", "GC_Percent"])
organelle_header = True
writer.writerow(
[
mol["assigned_molecule_location_type"],
round(mol["length"] / 1000000, 2),
mol["gc_percent"],
]
)
def extract_busco(file_in, writer):
with open(file_in, "r") as fin:
data = json.load(fin)
writer.writerow(["##BUSCO", data["lineage_dataset"]["name"]])
writer.writerow(["Summary", data["results"]["one_line_summary"]])
def extract_pacbio(qv, completeness, writer):
qval = 0
qv_name = None
for f in qv:
with open(f, "r") as fin:
data = csv.DictReader(fin, delimiter="\t")
for row in data:
if float(row["QV"]) > qval:
qval = float(row["QV"])
qv_name = remove_sample_T_suffix(os.path.basename(f).removesuffix(".qv"))
assert qv_name is not None, "No QV values found in %s" % qv
# The completeness has to be from the same specimen as the QV value
matching_completeness_files = []
for h in completeness:
comp_name = remove_sample_T_suffix(os.path.basename(h).removesuffix(".completeness.stats"))
if comp_name == qv_name:
matching_completeness_files.append(h)
assert matching_completeness_files, "No completeness files (%s) match for %s" % (completeness, qv_name)
comp = None
for h in matching_completeness_files:
with open(h, "r") as fin:
data = csv.DictReader(fin, delimiter="\t")
for row in data:
comp = float(row["% Covered"])
assert comp is not None, "No completeness values found in %s" % matching_completeness_files
writer.writerow(["##MerquryFK", qv_name])
writer.writerow(["QV", qval])
writer.writerow(["Completeness", comp])
def extract_mapped(sample, file_in, writer):
writer.writerow(["##HiC", remove_sample_T_suffix(sample)])
with open(file_in, "r") as fin:
for line in fin:
if "primary mapped" in line:
writer.writerow(["Primary_Mapped", re.search(r"\((.*?) :", line).group(1)])
def main(args=None):
args = parse_args(args)
out_dir = os.path.dirname(args.outcsv)
make_dir(out_dir)
with open(args.outcsv, "w") as fout:
writer = csv.writer(fout)
ncbi_stats(args.genome, args.sequence, writer)
if args.busco is not None:
extract_busco(args.busco, writer)
if args.qv and args.completeness is not None:
extract_pacbio(args.qv, args.completeness, writer)
if args.hic is not None:
for hic, flagstat in zip(args.hic, args.flagstat):
extract_mapped(hic, flagstat, writer)
if __name__ == "__main__":
sys.exit(main())