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-rw-r--r--scripts/dict_ontology_standardization/ncbi_countries.csv3
-rwxr-xr-xscripts/from_genbank_to_fasta_and_yaml.py36
2 files changed, 36 insertions, 3 deletions
diff --git a/scripts/dict_ontology_standardization/ncbi_countries.csv b/scripts/dict_ontology_standardization/ncbi_countries.csv
index 6918493..7e83564 100644
--- a/scripts/dict_ontology_standardization/ncbi_countries.csv
+++ b/scripts/dict_ontology_standardization/ncbi_countries.csv
@@ -127,6 +127,7 @@ Hungary,http://www.wikidata.org/entity/Q28
Iceland,http://www.wikidata.org/entity/Q189
Icelandic Commonwealth,http://www.wikidata.org/entity/Q62389
India,http://www.wikidata.org/entity/Q668
+India: Ahmedabad,http://www.wikidata.org/entity/Q1070
India: Kerala State,http://www.wikidata.org/entity/Q1186
India: Rajkot,http://www.wikidata.org/entity/Q1815245
Indonesia,http://www.wikidata.org/entity/Q252
@@ -288,6 +289,7 @@ USA: KY,http://www.wikidata.org/entity/Q1603
USA: LA,http://www.wikidata.org/entity/Q1588
"USA: New Orleans, LA",https://www.wikidata.org/wiki/Q34404
USA: MA,http://www.wikidata.org/entity/Q771
+USA: Massachusetts,http://www.wikidata.org/entity/Q771
USA: MD,http://www.wikidata.org/entity/Q1391
USA: ME,http://www.wikidata.org/entity/Q724
USA: MI,http://www.wikidata.org/entity/Q1166
@@ -320,6 +322,7 @@ USA: TN,http://www.wikidata.org/entity/Q1509
USA: TX,http://www.wikidata.org/entity/Q1439
USA: UT,http://www.wikidata.org/entity/Q829
USA: VA,http://www.wikidata.org/entity/Q1370
+USA: Virginia,http://www.wikidata.org/entity/Q1370
USA: VT,http://www.wikidata.org/entity/Q16551
USA: WA,http://www.wikidata.org/entity/Q1223
USA: WI,http://www.wikidata.org/entity/Q1537
diff --git a/scripts/from_genbank_to_fasta_and_yaml.py b/scripts/from_genbank_to_fasta_and_yaml.py
index befd64d..65adb00 100755
--- a/scripts/from_genbank_to_fasta_and_yaml.py
+++ b/scripts/from_genbank_to_fasta_and_yaml.py
@@ -1,5 +1,11 @@
#!/usr/bin/env python3
+import argparse
+parser = argparse.ArgumentParser()
+parser.add_argument('--skip-request', action='store_true', help='skip metadata and sequence request', required=False)
+parser.add_argument('--only-missing-id', action='store_true', help='download only missing id', required=False)
+args = parser.parse_args()
+
from Bio import Entrez
Entrez.email = 'another_email@gmail.com'
@@ -7,6 +13,7 @@ import xml.etree.ElementTree as ET
import json
import os
import requests
+import sys
from datetime import date
from dateutil.parser import parse
@@ -31,9 +38,27 @@ def chunks(lst, n):
for i in range(0, len(lst), n):
yield lst[i:i + n]
-if not os.path.exists(dir_metadata):
- os.makedirs(dir_metadata)
+if os.path.exists(dir_metadata):
+ print("The directory '{}' already exists.".format(dir_metadata))
+
+ if not args.skip_request:
+ print("\tTo start the request, delete the directory '{}' or specify --skip-request.".format(dir_metadata))
+ sys.exit(-1)
+
+
+accession_already_downloaded_set = []
+if os.path.exists(dir_fasta_and_yaml):
+ print("The directory '{}' already exists.".format(dir_fasta_and_yaml))
+ if not args.only_missing_id:
+ print("To start the download, delete the directory '{}' or specify --only-missing-id.".format(dir_fasta_and_yaml))
+ sys.exit(-1)
+
+ accession_already_downloaded_set = set([x.split('.yaml')[0].split('.')[0] for x in os.listdir(dir_fasta_and_yaml) if x.endswith('.yaml')])
+ print('There are {} accession already downloaded.'.format(len(accession_already_downloaded_set)))
+
+
+if not os.path.exists(dir_metadata):
# Take all the ids
id_set = set()
@@ -70,6 +95,11 @@ if not os.path.exists(dir_metadata):
print('DB: NCBI Virus', today_date, '-->', new_ids, 'new IDs from', len(tmp_list), '---> Total unique IDs:', len(id_set))
+ if len(accession_already_downloaded_set) > 0:
+ id_set = id_set.difference(accession_already_downloaded_set)
+ print('There are {} missing IDs to download.'.format(len(id_set)))
+
+ os.makedirs(dir_metadata)
for i, id_x_list in enumerate(chunks(list(id_set), num_ids_for_request)):
path_metadata_xxx_xml = os.path.join(dir_metadata, 'metadata_{}.xml'.format(i))
print('Requesting {} ids --> {}'.format(len(id_x_list), path_metadata_xxx_xml))
@@ -353,4 +383,4 @@ if len(missing_value_list) > 0:
with open('missing_terms.tsv', 'w') as fw:
fw.write('\n'.join(missing_value_list))
-print('Num. sequences with length >= {} bp: {}'.format(min_len_to_count, num_seq_with_len_ge_X_bp))
+print('Num. new sequences with length >= {} bp: {}'.format(min_len_to_count, num_seq_with_len_ge_X_bp))