"""Search for term in EBI to get accessions that link to genomic metadata in XML format"""

from joblib import Parallel, delayed

import requests

from tqdm import tqdm

import xmltodict

with open("ENA_READS_SUPPRESSED.txt", "r") as inAccess:

Ids = inAccess.read().splitlines()

def search_ENA(Id):

if Id == "ND":

return None

apiURL = "https://www.ebi.ac.uk/ebisearch/ws/rest/sra-sample?query={}&fields=acc,description,name&size=100".format(Id.replace("#", "%23"))

urlResponse = requests.get(apiURL)

accession_metadata = dict(xmltodict.parse(urlResponse.text))

try:

if accession_metadata["result"]["hitCount"] == "0":

apiURL = "https://www.ebi.ac.uk/ebisearch/ws/rest/wgs_masters?query={}&fields=acc,description,name&size=100".format(Id.replace("#", "%23"))

urlResponse = requests.get(apiURL)

accession_metadata = dict(xmltodict.parse(urlResponse.text))

if accession_metadata["result"]["hitCount"] == "0":

if "NC_" in Id:

with open("ESC_NCBI_ASSEMBLIES.txt", "a") as assem:

assem.write(Id + "\n")

else:

with open("ESC_NOT_FOUND.txt", "a") as suppressed:

suppressed.write(Id + "\n")

else:

try:

access = accession_metadata["result"]["entries"]['entry']["@id"]

except:

if "NC_" in Id:

with open("ESC_NCBI_ASSEMBLIES.txt", "a") as assem:

assem.write(Id + "\n")

else:

with open("ESC_NOT_FOUND.txt", "a") as suppressed:

suppressed.write(Id + "\n")

txtURL = "https://www.ebi.ac.uk/ena/browser/api/embl/{}?lineLimit=1000".format(access)

urlResponse = requests.get(txtURL).text.splitlines()

for resp in urlResponse:

if "BioSample" in resp:

biosample = resp.split(" ")[4].replace(".", "")

with open("ESC_FOUND.txt", "a") as found:

found.write(Id + "\n")

with open("ESC_SEARCH_FOUND_ACCESSIONS.txt", "a") as identified:

identified.write(biosample + "\n")

return biosample

else:

access = accession_metadata["result"]["entries"]['entry']["@id"]

with open("ESC_FOUND.txt", "a") as found:

found.write(Id + "\n")

with open("ESC_SEARCH_FOUND_ACCESSIONS.txt", "a") as identified:

identified.write(access + "\n")

return access

except:

with open("ESC_NOT_FOUND.txt", "a") as suppressed:

suppressed.write(Id + "\n")

job_list = [

Ids[i:i + 20] for i in range(0, len(Ids), 20)

]

foundAccessions = []

for job in tqdm(job_list):

foundAccessions += Parallel(n_jobs=20)(delayed(search_ENA)(i) for i in job)