Support for some binary sequence formats for BioPython.
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  1. BinSeqs - Support for binary sequence formats in Bioython
  2. =========================================================
  3. BinSeqs is a Python package intended to enrich the SeqIO
  4. framework from [Biopython](https://biopython.org/) by adding
  5. support for some binary sequence formats.
  6. Deprecation Warning
  7. -------------------
  8. This code has now been merged into Biopython. Starting from
  9. Biopython release 1.75, all you need to do to support the formats
  10. below is to load the `Bio.SeqIO` module.
  11. Consequently, this project will no longer be maintained. It will
  12. remain available online but will not be updated. All improvements
  13. and bug fixes will occur in the Biopython repository.
  14. You can still use this module until Biopython 1.75 is released and
  15. available on your system. After that, loading the `incenp.bio.seqio`
  16. module will be a no-op and a DeprecationWarning will be emitted.
  17. Formats supported
  18. -----------------
  19. * `xdna` format, used by _DNA Strider_ and
  20. [Serial Cloner](http://serialbasics.free.fr/Serial_Cloner.html):
  21. reading and writing supported
  22. * `snapgene` format, used by [SnapGene](https://www.snapgene.com/):
  23. reading support only
  24. * `gck` format, used by [Gene Construction Kit](http://www.textco.com/gene-construction-kit.php):
  25. reading support only
  26. Usage
  27. -----
  28. The BinSeqs parsers and writers are not designed to be used
  29. independently and should instead be used through the Biopython's
  30. SeqIO module.
  31. Simply import the `incenp.bio.seqio` module to make the parsers
  32. and writers available to Biopython's SeqIO:
  33. from Bio import SeqIO
  34. import incenp.bio.seqio
  35. records = list(SeqIO.parse('snapgene_file.dna', 'snapgene'))
  36. SeqIO.write(records, 'serialcloner_file.xdna', 'xdna')
  37. Copying
  38. -------
  39. BinSeqs is free software and distributed under the terms of
  40. a BSD-like license. The full license is included in the
  41. [LICENSE.txt file](LICENSE.txt) of the source distribution.
  42. Homepage
  43. --------
  44. The project is located at https://incenp.org/dvlpt/binseqs.html
  45. (homepage) and https://git.incenp.org/damien/binseqs (repository
  46. and bug tracker).