aboutsummaryrefslogtreecommitdiff
path: root/scripts/from_genbank_to_fasta_and_yaml.py
diff options
context:
space:
mode:
authorAndreaGuarracino2020-06-06 16:12:44 +0200
committerAndreaGuarracino2020-06-06 16:12:44 +0200
commit9f31ac441e69d4e07bf93235cfa0459a077fb00c (patch)
treeaa6631b9754690f56064e6ca4ec370c4d12d5681 /scripts/from_genbank_to_fasta_and_yaml.py
parent278b1e7ccbc8b56e6e9b3413840b18f3ce0f36e7 (diff)
downloadbh20-seq-resource-9f31ac441e69d4e07bf93235cfa0459a077fb00c.tar.gz
bh20-seq-resource-9f31ac441e69d4e07bf93235cfa0459a077fb00c.tar.lz
bh20-seq-resource-9f31ac441e69d4e07bf93235cfa0459a077fb00c.zip
fixed collection-date management using a parser
Diffstat (limited to 'scripts/from_genbank_to_fasta_and_yaml.py')
-rwxr-xr-xscripts/from_genbank_to_fasta_and_yaml.py4
1 files changed, 2 insertions, 2 deletions
diff --git a/scripts/from_genbank_to_fasta_and_yaml.py b/scripts/from_genbank_to_fasta_and_yaml.py
index fc09615..9c8e9b9 100755
--- a/scripts/from_genbank_to_fasta_and_yaml.py
+++ b/scripts/from_genbank_to_fasta_and_yaml.py
@@ -8,8 +8,8 @@ import json
import os
import requests
-from dateutil import parser
from datetime import date
+from dateutil.parser import parse
num_ids_for_request = 100
@@ -312,7 +312,7 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml)
GBQualifier_value_text_list = GBQualifier_value_text.split('-')
if GBQualifier_value_text_list[1].isalpha():
- date_to_write = GBQualifier_value_text_list[1] + '-' + GBQualifier_value_text_list[0] + '-' + GBQualifier_value_text_list[2]
+ date_to_write = parse(GBQualifier_value_text).strftime('%Y-%m-%d')
info_for_yaml_dict['sample']['collection_date'] = date_to_write
elif GBQualifier_name_text in ['lat_lon', 'country']: