[Biopython] Support for Xdna and SnapGene formats

[Damien Goutte-Gattat]

Hi Biopython folks,

I frequently have to work with sequence files generated by either
SerialCloner or SnapGene and would like to see the corresponding
file formats supported by Biopython’s SeqIO.

Back in 2015, Helena Rasche volunteered to add a SnapGene/ZTR
module [1], but unless I missed something, as of today there is no
such module in Biopython.

Therefore I wrote my own modules [2] to add support for the Xdna
file format (used by DNA Strider and Serial Cloner) and the
SnapGene file format.

If you want to try them, simply import `incenp.bio.seqio` and then
use Biopython’s SeqIO functions as usual:

  from Bio import SeqIO
  import incenp.bio.seqio

  records = list(SeqIO.read('serialcloner_file.xdna', 'xdna'))
  records = list(SeqIO.read('snapgene_file.dna', 'snapgene'))

For what it’s worth, I have been using those modules for nearly a
year and they seem to be working quite fine, although I would not
dare to claim they are bug-free.

Is there an interest to have those parsers incorporated into
Biopython? If so, I can do the necessary changes and prepare a
proper pull request.


Regards,

- Damien


[1] https://github.com/biopython/biopython/issues/602

[2] https://incenp.org/dvlpt/gitweb/?p=binseqs.git;a=summary
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