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Changed card to utilise .tar.bz2 from .tar.gz #201

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merged 1 commit into from
Nov 8, 2017
Merged

Changed card to utilise .tar.bz2 from .tar.gz #201

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4 changes: 2 additions & 2 deletions ariba/ref_genes_getter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,7 @@ def __init__(self, ref_db, version=None, debug=False):
def _get_card_versions(self, tmp_file):
print('Getting available CARD versions')
common.download_file('https://card.mcmaster.ca/download', tmp_file, max_attempts=self.max_download_attempts, sleep_time=self.sleep_time, verbose=True)
p = re.compile(r'''href="(/download/.*?broad.*?v([0-9]+\.[0-9]+\.[0-9]+)\.tar\.gz)"''')
p = re.compile(r'''href="(/download/.*?broad.*?v([0-9]+\.[0-9]+\.[0-9]+)\.tar\.bz2)"''')
versions = {}

with open(tmp_file) as f:
Expand Down Expand Up @@ -85,7 +85,7 @@ def _get_from_card(self, outprefix):

print('Getting version', self.version)
card_tarball_url = versions[key]
card_tarball = 'card.tar.gz'
card_tarball = 'card.tar.bz2'
print('Working in temporary directory', tmpdir)
print('Downloading data from card:', card_tarball_url, flush=True)
common.syscall('wget -O ' + card_tarball + ' ' + card_tarball_url, verbose=True)
Expand Down