Example #1
0
 def from_vdb(self, virus):
     from vdb_download import vdb_download
     from Bio.SeqRecord import SeqRecord
     from Bio.Seq import Seq
     myvdb = vdb_download(virus=virus)
     myvdb.download(output=False)
     self.raw_seqs={}
     for v in myvdb.viruses:
         attr = {k:v[k] for k in v if k!='sequence'}
         seq = SeqRecord(Seq(v['sequence']), id=attr['strain'], name=attr['strain'], description=attr['strain'])
         seq.attributes = attr
         self.raw_seqs[attr['strain']] = seq