[Biopython] Lightweight version of Biopython?

[Erick Matsen]

Peter--


Thank you for the complete response.

We will have to have a run-off between a biopython install and our
homegrown file format converters.


Erick



On Wed, Nov 3, 2010 at 5:38 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> On Wed, Nov 3, 2010 at 12:16 PM, Erick Matsen <matsen at fhcrc.org> wrote:
>> Hello Peter--
>>
>> Thanks for the quick response.
>>
>> Perhaps "heavy" isn't the right word, but it definitely seems overkill
>> when all we want to do is convert between three file formats (FASTA,
>> phylip, and Stockholm). Furthermore, something little we can include
>> directly in the project (with credit given where it is due) would be
>> ideal. An installation script could look for Biopython and use it if
>> it's there, or use the lite version if not.
>>
>
> Hi Erick,
>
> Under our licence you could take a snapshot copy of the bits you need
> and include them in your application. However, the bits you'd need for
> Bio.AlignIO would basically be the core sequence stuff in Biopython
> (at very least Bio.Alphabet, Bio.Seq, Bio.SeqRecord, Bio.SeqFeature,
> Bio.SeqIO, Bio.Align, and Bio.AlignIO). This adds up to a lot of files,
> but would be possible... How are you distributing your application? If
> using py2exe or a source code bundle you could in theory bundle in
> (part of) Biopython.
>
> If using pip or easy_install (i.e. PyPi packages) then it *should* take
> care of a dependency on Biopython.
>
> Suppose hypothetically with had a "lite" or "seq-core" version of
> Biopython containing Bio.SeqIO, Bio.AlignIO and their dependencies
> (but excluding Bio.PDB, Bio.Phylo, Bio.Cluster, Bio.Blast, BioSQL etc).
> The download would be smaller (say a third of the size), but it isn't that
> big to start with. There wouldn't be the (soft) dependency on NumPy.
> Neither of these benefits seems compelling to me.
>
> Regards,
>
> Peter
>