aboutsummaryrefslogtreecommitdiff
path: root/scripts/download_genbank_data
diff options
context:
space:
mode:
authorAndreaGuarracino2020-11-13 22:04:36 +0100
committerAndreaGuarracino2020-11-13 22:04:36 +0100
commita5f5a85b9db5e84f3680e85b7116f324fd6d2e2e (patch)
treee2544a90619a2001a5a3cb2332c681d0128ff1a5 /scripts/download_genbank_data
parent852fbbd14a174addcfe729ab2b54e556228984a4 (diff)
downloadbh20-seq-resource-a5f5a85b9db5e84f3680e85b7116f324fd6d2e2e.tar.gz
bh20-seq-resource-a5f5a85b9db5e84f3680e85b7116f324fd6d2e2e.tar.lz
bh20-seq-resource-a5f5a85b9db5e84f3680e85b7116f324fd6d2e2e.zip
to not create YAML files with date before 2019 December
Diffstat (limited to 'scripts/download_genbank_data')
-rwxr-xr-xscripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py12
1 files changed, 11 insertions, 1 deletions
diff --git a/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py b/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py
index 5a8a336..8fbacd1 100755
--- a/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py
+++ b/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py
@@ -18,7 +18,7 @@ import json
import os
import requests
-from datetime import date
+from datetime import date, datetime
from dateutil.parser import parse
import sys
@@ -27,6 +27,7 @@ from utils import is_integer, chunks, check_and_get_ontology_dictionaries
num_ids_for_request = 100
+min_acceptable_collection_date = datetime(2019, 12, 1)
dir_metadata = 'metadata_from_nuccore'
dir_fasta_and_yaml = 'fasta_and_yaml'
@@ -404,6 +405,15 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml)
if accession_version not in not_created_accession_dict:
not_created_accession_dict[accession_version] = []
not_created_accession_dict[accession_version].append('collection_date not found')
+ else:
+ year, month, day = [int(x) for x in info_for_yaml_dict['sample']['collection_date'].split('-')]
+
+ collection_date_in_yaml = datetime(year, month, day)
+
+ if collection_date_in_yaml < min_acceptable_collection_date:
+ if accession_version not in not_created_accession_dict:
+ not_created_accession_dict[accession_version] = []
+ not_created_accession_dict[accession_version].append('collection_date too early')
if 'authors' not in info_for_yaml_dict['submitter']:
if accession_version not in not_created_accession_dict: