From 9437f4637b10316765422ce30255b3aa2d1e267b Mon Sep 17 00:00:00 2001 From: Hui Lan Date: Sat, 12 Apr 2025 15:29:01 +0800 Subject: Save ENA records to XML files under Data/temp/ --- Code/download_ena_records.py | 19 +++++++++++++++++-- 1 file changed, 17 insertions(+), 2 deletions(-) (limited to 'Code/download_ena_records.py') diff --git a/Code/download_ena_records.py b/Code/download_ena_records.py index 0f0cf30..b535c3e 100644 --- a/Code/download_ena_records.py +++ b/Code/download_ena_records.py @@ -1,10 +1,25 @@ -accession = 3702 -types = ['read_run', 'read_expriment', 'sample', 'study'] +# Download ENA records so that we can discover newly uploaded data +# 2025-04-12 +# Hui + +import os +import sys +import time +from configure import TEMP_DIR, UPDATE_NETWORK_LOG_FILE +from log import write_log_file +accession = 3702 # arabidopsis +types = ['read_run', 'read_expriment', 'sample', 'study'] for t in types: url = f'https://www.ebi.ac.uk/ena/browser/api/xml/links/taxon?accession={accession}&result={t}' print(url) + if not os.path.exists(TEMP_DIR): + sys.exit() + cmd = 'wget "%s" -O %s' % (url, os.path.join(TEMP_DIR, 'ena_'+t+'.xml')) # save XML data to file + os.system(cmd) + time.sleep(5) +write_log_file('ENA records updated. Check folder %s' % (TEMP_DIR), UPDATE_NETWORK_LOG_FILE) #https://www.ebi.ac.uk/ena/browser/api/xml/links/taxon?accession=3702&result=read_run #https://www.ebi.ac.uk/ena/browser/api/xml/links/taxon?accession=3702&result=read_experiment -- cgit v1.2.1