From 7f69842ad80e6fd36aea89ef2431ace5d442fd04 Mon Sep 17 00:00:00 2001 From: martinghunt Date: Thu, 5 May 2016 09:37:02 +0000 Subject: [PATCH] Update card from 1.0.5 to 1.0.6 --- ariba/ref_genes_getter.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/ariba/ref_genes_getter.py b/ariba/ref_genes_getter.py index 8f9997d1..c2168b7f 100644 --- a/ariba/ref_genes_getter.py +++ b/ariba/ref_genes_getter.py @@ -49,7 +49,7 @@ def _get_from_card(self, outprefix): except: raise Error('Error mkdir/chdir ' + tmpdir) - card_version = '1.0.5' + card_version = '1.0.6' card_tarball_url = 'https://card.mcmaster.ca/download/0/broadsteet-v' + card_version + '.tar.gz' card_tarball = 'card.tar.gz' print('Working in temporary directory', tmpdir) @@ -241,23 +241,23 @@ def _get_from_vfdb(self, outprefix): outprefix = os.path.abspath(outprefix) tmpdir = outprefix + '.tmp.download' current_dir = os.getcwd() - + try: os.mkdir(tmpdir) os.chdir(tmpdir) except: raise Error('Error mkdir/chdir ' + tmpdir) - + zipfile = 'VFDB_setA_nt.fas.gz' self._download_file('http://www.mgc.ac.cn/VFs/Down/VFDB_setA_nt.fas.gz', zipfile) common.syscall('gunzip ' + zipfile) os.chdir(current_dir) print('Extracted files.') - + final_fasta = outprefix + '_VFDB.fa' shutil.move(tmpdir+'/VFDB_setA_nt.fas',final_fasta) shutil.rmtree(tmpdir) - + print('Extracted core DNA sequence dataset. Final file is called', final_fasta, end='\n\n') print('You can use it with ARIBA like this:') print('ariba prepareref --presabs', final_fasta, 'output_directory\n')