From 46f520cb6ba2782544d926dbd415e1dbe3f0332d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E8=B0=B7=E6=B2=A2=E9=9D=96=E6=B4=8B?= Date: Fri, 29 Jan 2021 10:37:32 +0900 Subject: [PATCH] dfast_file_downloader.py updated (http download from NCBI) --- scripts/dfast_file_downloader.py | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/scripts/dfast_file_downloader.py b/scripts/dfast_file_downloader.py index 79cc829..2063f94 100755 --- a/scripts/dfast_file_downloader.py +++ b/scripts/dfast_file_downloader.py @@ -53,6 +53,8 @@ "TIGR": "https://ftp.ncbi.nlm.nih.gov/hmm/TIGRFAMs/release_15.0/TIGRFAMs_15.0_HMM.LIB.gz" } +cdd_url = "https://ftp.ncbi.nlm.nih.gov//pub/mmdb/cdd/little_endian/DBNAME_LE.tar.gz" + description = """\ DFAST file downloader\n\ @@ -114,8 +116,8 @@ def retrieve_hmm(db_name, out_dir="."): logger.info("\tDownloading {}".format(target_url)) return output_file - -def retrieve_cdd(db_name, out_dir="."): +# deprecated +def retrieve_cdd_ftp(db_name, out_dir="."): ftp = FTP(host=ncbi_ftp_server) logger.info("\tLogging in to the FTP server. {}".format(ncbi_ftp_server + cdd_directory)) ftp.login() @@ -129,6 +131,14 @@ def retrieve_cdd(db_name, out_dir="."): ftp.quit() return output_file +def retrieve_cdd(db_name, out_dir="."): + target_url = cdd_url.replace("DBNAME", db_name) + target_file = os.path.basename(target_url) + output_file = os.path.join(out_dir, target_file) + request.urlretrieve(target_url, output_file) + logger.info("\tDownloading {}".format(target_url)) + return output_file + def retrieve_assembly(accession, out_dir="."): def _get_ftp_directory(accession): path1, path2, path3, path4 = accession[0:3], accession[4:7], accession[7:10], accession[10:13]