def register_rfam_tasks(handler, params, databases):
rfam = databases['Rfam']
archive_fn = '{0}.{1}'.format(rfam['filename'], rfam['fileformat'])
target_fn = path.join(handler.directory, rfam['filename'])
dl_task = get_download_task(rfam['url'], archive_fn, md5=rfam['md5'])
gz_task = get_gunzip_task(archive_fn, target_fn)
handler.register_task('download:Rfam',
dl_task,
files={'Rfam-gz': archive_fn})
handler.register_task('gunzip:Rfam', gz_task, files={'Rfam': target_fn})
handler.register_task('cmpress:Rfam',
CMPressTask().task(target_fn, params=params))
return handler
def register_orthodb_tasks(handler, params, databases):
orthodb = databases['OrthoDB']
archive_fn = '{0}.{1}'.format(orthodb['filename'], orthodb['fileformat'])
target_fn = path.join(handler.directory, orthodb['filename'])
dl_task = get_download_task(orthodb['url'], archive_fn, md5=orthodb['md5'])
gz_task = get_gunzip_task(archive_fn, target_fn)
handler.register_task('download:OrthoDB',
dl_task,
files={'OrthoDB-gz': archive_fn})
handler.register_task('gunzip:OrthoDB',
gz_task,
files={'OrthoDB': target_fn})
handler.register_task(
'lastdb:OrthoDB',
LastDBTask().task(target_fn, target_fn, prot=True, params=params))
return handler
def register_pfam_tasks(handler, params, databases):
pfam_A = databases['Pfam-A']
archive_fn = '{0}.{1}'.format(pfam_A['filename'], pfam_A['fileformat'])
target_fn = path.join(handler.directory, pfam_A['filename'])
dl_task = get_download_task(pfam_A['url'], archive_fn, md5=pfam_A['md5'])
gz_task = get_gunzip_task(archive_fn, target_fn)
handler.register_task('download:Pfam-A',
dl_task,
files={'Pfam-A-gz': archive_fn})
handler.register_task('gunzip:Pfam-A',
gz_task,
files={'Pfam-A': target_fn})
handler.register_task('hmmpress:Pfam-A',
HMMPressTask().task(target_fn, params=params))
return handler