[BioPython] question regarding unicode, biopython Seq object, DAS

[Michiel de Hoon]

Ann Loraine wrote:
> My sax parser delivers character (sequence) data as unicode, but when
> I make a Seq object from the unicode string and then try to reverse
> complement the sequence, I get an exception:

Can you convert the unicode string to a regular string before creating 
the Seq object? As in

 >>> from Bio.Alphabet import IUPAC
 >>> from Bio.Seq import Seq
 >>> s = u'atcg'
 >>> s = str(s)
 >>> s = Seq(s, IUPAC.unambiguous_dna)
 >>> s.reverse_complement()
Seq('cgat', IUPACUnambiguousDNA())
 >>>

By the way, you can also use reverse_complement on a string directly:

 >>> from Bio.Seq import reverse_complement
 >>> s = 'atcg'
 >>> reverse_complement(s)
'cgat'
 >>>


--Michiel.