def run(self):
url = "http://pfam.sanger.ac.uk/family/alignment/download/gzipped?acc=%s&alnType=%s"
url %= self.params['id'], ('full' if self.params['full'] else 'seed')
tmp = StringIO.StringIO(urllib2.urlopen(url).read())
alignment = gzip.GzipFile(fileobj=tmp)
msa = StockholmFormatMSA.from_text(alignment)
path = "%s-%s" % (self.params['id'], ('full' if self.params['full'] else 'seed'))
self.target.set_msa(msa.sequences, path, msa.ids, msa.descriptions)
def run(self):
msa = StockholmFormatMSA.from_text(open(self.params['location']))
self.target.set_msa(msa.sequences, self.params['location'], msa.ids, msa.descriptions)