Python StockholmFormatMSA.from_text Examples

Example #1

File: __init__.py Project: yohell/msaview

 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)

Example #2

File: __init__.py Project: yohell/msaview

 def run(self):
     msa = StockholmFormatMSA.from_text(open(self.params['location']))
     self.target.set_msa(msa.sequences, self.params['location'], msa.ids, msa.descriptions)