[Biopython-dev] DAS client in biopython

[Andrea Pierleoni]

>
> So what DAS calls a sequence is closer to Biopython's SeqRecord
> than Biopython Seq object? Hmm - that could cause confusion,
> whatever you call your class.
>

here there is an example of a DASSEQUENCE

<?xml version="1.0" standalone='no'?>
<!DOCTYPE DASSEQUENCE SYSTEM "http://www.biodas.org/dtd/dassequence.dtd">
<DASSEQUENCE>
<SEQUENCE id="P00280" start="1" stop="149" moltype="Protein"
version="8f29b1d09f48ec8e9909593052dcfaec">MLAKATLAIVLSAASLPVLAAQCEATIESNDAMQYNLKEMVVDKSCKQFTVHLKHVGKMAKVAMGHNWVLTKEADKQGVATDGMNAGLAQDYVKAGDTRVIAHTKVIGGGESDSVTFDVSKLTPGEAYAYFCSFPGHWAMMKGTLKLSN</SEQUENCE>
</DASSEQUENCE>

it is basically a Seq object with some metadata associated that I'm keeping.
the moltype is used to set the Alphabet. It has an ID so it could also
fit a seqrecord, but the DASseq class should not be used outside of
DAS.py.

Than you can link to this sequence, feature and annotations that are
parsed from DASGFF XML response. the big confusion here is that both
SeqRecord anntotations and features comes with DASGFF.
annotations has start and end position equal to 0.

>> Most of the time this class shouden0t be accessed. and a clean
>> SeqRecord object can be obtained using the "fetch_to_seqrec"
>> method in DASregistry.
>
> I'll take another look at your code later.
>


any comment is welcome, thanks

Andrea