# Genbank XML parser from collections import namedtuple import dateutil from dateutil.parser import parse as dateparse from dateutil.tz import gettz import os import re import sys import types import xml.etree.ElementTree as ET class GBError(Exception): pass """ Example of an output JSON: { "id": "placeholder", "host": { "host_species": "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, "sample": { "sample_id": "MT890462.1", "source_database_accession": [ "http://identifiers.org/insdc/MT890462.1#sequence" ], "collection_location": "http://www.wikidata.org/entity/Q649", "collection_date": "2020-04-17", "collecting_institution": "N.A.Kovtun Clinical Hospital 1 of Departament of President Affairs" }, "virus": { "virus_strain": "SARS-CoV-2/human/RUS/20200417_10/2020", "virus_species": "http://purl.obolibrary.org/obo/NCBITaxon_2697049" }, "technology": { "assembly_method": "http://purl.obolibrary.org/obo/GENEPIO_0001628", "alignment_protocol": "bowtie2 v. 2.3.4", "sample_sequencing_technology": [ "http://purl.obolibrary.org/obo/OBI_0000759" ] }, "submitter": { "authors": [ "Blagodatskikh,K.A." ], "submitter_name": [ "R&D" ], "submitter_address": "Pirogov Russian National Research Medical University, Ostrovityanova 1, Moscow 117997, Russia" } } Note: missing data should be None! Do not fill in other data by 'guessing'. """ def get_metadata(id, gbseq): host = types.SimpleNamespace() sample = types.SimpleNamespace() submitter = types.SimpleNamespace() warnings = [] def warn(msg): print(f"WARNING: {msg}",file=sys.stderr) warnings.append(msg) host.host_species = "http://purl.obolibrary.org/obo/NCBITaxon_9606" sample.sample_id = id sample.database = "https://www.ncbi.nlm.nih.gov/genbank/" sample.source_database_accession = f"http://identifiers.org/insdc/{id}#sequence" # # country # USA: Cruise_Ship_1, California # sample.collection_location = "FIXME" submitter.authors = [n.text for n in gbseq.findall(".//GBAuthor")] # --- Dates n = gbseq.find("./GBSeq_create-date") creation_date = dateparse(n.text).date() n = gbseq.find("./GBSeq_update-date") update_date = dateparse(n.text).date() n = gbseq.find(".//GBQualifier/GBQualifier_name/[.='collection_date']/../GBQualifier_value") try: date = dateparse(n.text).date() sample.collection_date = str(date) except dateutil.parser._parser.ParserError as e: warn("No collection_date: ",str(e)) sample.collection_date = None except AttributeError: warn("Missing collection_date") sample.collection_date = None info = { 'id': 'placeholder', 'update_date': str(update_date), 'host': host, 'sample': sample, #'virus': virus, #'technology': technology, 'submitter': submitter, 'warnings': warnings, } print(info) return True,info def get_sequence(id, gbseq): seq = None count = 0 for gbseq_sequence in gbseq.findall('./GBSeq_sequence'): count += 1 if count > 1: raise GBError(f"Expected one sequence for {id}") seq = gbseq_sequence.text.upper() print(f"SEQ: size={len(seq)}",seq[0:30]) if len(seq) < 20_000: raise GBError(f"Sequence too short") return seq