[Biopython-dev] [Wg-phyloinformatics] GSoC Weekly Update: PhyloXML for Biopython
Eric Talevich
eric.talevich at gmail.com
Mon Jun 22 13:08:05 UTC 2009
On Mon, Jun 22, 2009 at 7:29 AM, Peter <biopython at maubp.freeserve.co.uk>wrote:
> On Thu, Jun 18, 2009 at 12:17 AM, Eric Talevich <eric.talevich at gmail.com>
> wrote:> *SeqRecord transformation*
> >
>
> I was just having a very brief scan over the commits that my RSS
> feed had - and noticed this bit:
>
> + # Unpack record.features
> + if record.features:
> + kwargs['domain_architecture'] = DomainArchitecture(
> + domains=[ProteinDomain({
> + 'from': feat.location.start + 1,
> + 'to': feat.location.end + 1,
> + 'confidence':
> feat.qualifiers.get('confidence')
> + }, value=feat.id)
> + for feat in record.features],
> + length=len(record.seq)
> + )
>
> I can understand a +/- one to the start location (moving between
> Python zero based counting and normal one based counts), but
> why would the end location also change?
>
> Peter
>
Er, it wouldn't. Oops.
On that note, how do you feel about specifying biology-style indexes in
PhyloXML.ProteinDomain, and switching to zero-based indexes when converting
to SeqFeature? Would it be better to use zero-based indexes in ProteinDomain
and substract 1 from the start position during parsing?
Thanks,
Eric
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