"""Sample one isolate per GPSC"""

import json

from tqdm import tqdm

with open("GPS_poppunk.txt", "r") as GPSFile:

isolateList = GPSFile.read().splitlines()

with open("GPS_metadata.json", "r") as metafile:

GPSmetadata = json.loads(metafile.read())

metadataIsolates = []

for accession, data in GPSmetadata.items():

metadataIsolates.append(data["Lane_Id"])

GPSC_counts = {}

subsamples = []

total_count = 0

for row in isolateList:

splitRow = row.split("\t")

laneID = splitRow[0].split("_")

laneID = "#".join(["_".join(laneID[0:2])] + [laneID[2]])

total_count += 1

if not int(splitRow[1]) in GPSC_counts.keys():

GPSC_counts[int(splitRow[1])] = 1

if laneID in metadataIsolates:

subsamples.append(laneID)

else:

GPSC_counts[int(splitRow[1])] += 1

with open("GPS_samples.txt", "w") as sampleOut:

sampleOut.write("\n".join(subsamples))