import json

import sys

from tqdm import tqdm

def get_options():

import argparse

parser = argparse.ArgumentParser(prog='extract_entrez_reads')

io_opts = parser.add_argument_group('input')

io_opts.add_argument("--assembly-metadata",

dest="assemblies",

required=True,

help='Isolate assembly metadata output by extact_asembly_stats.py',

type=str)

io_opts.add_argument("--read-metadata",

dest="reads",

required=True,

help='Isolate read metadata output by extact_read_metadata.py',

type=str)

args = parser.parse_args()

return (args)

def main():

"""Main function. Parses command line args and calls functions."""

args = get_options()

sys.stderr.write("\nImporting metadata files\n")

with open(args.assemblies, "r") as metaFile:

metadata = json.loads(metaFile.read())["information"]

with open(args.reads, "r") as metaFile:

metadata += json.loads(metaFile.read())["information"]

sys.stderr.write("\nIterating through isolates and extracting assembly stats\n")

data = {}

for isolate in tqdm(metadata):

if "coli" in isolate["Organism_name"]:

isolate_stats = {}

isolate_stats["contig_N50"] = isolate["contig_stats"]["N50"]

isolate_stats["gc_content"] = isolate["contig_stats"]["gc_content"]

isolate_stats["contig_mean_length"] = isolate["contig_stats"]["mean"]

isolate_stats["contig_count"] = isolate["contig_stats"]["sequence_count"]

isolate_stats["genome_length"] = isolate["contig_stats"]["total_bps"]

isolate_stats["scaffold_N50"] = isolate["contig_stats"]["N50"]

isolate_stats["scaffold_mean_length"] = isolate["scaffold_stats"]["mean"]

isolate_stats["scaffold_count"] = isolate["scaffold_stats"]["sequence_count"]

try:

data[isolate["isolateNameUnderscore"]] = isolate_stats

except KeyError:

data[isolate["isolateName"]] = isolate_stats

with open("ESC_population_assembly_stats.json", "w") as outJSON:

outJSON.write(json.dumps(data))

sys.exit(0)

if __name__ == '__main__':

main()