[BioPython] Removing Bio.FormatIO ?
Peter
biopython at maubp.freeserve.co.uk
Tue Sep 18 08:12:02 UTC 2007
Having looked at the Bio.FormatIO code in more detail, a simple
deprecation warning isn't an option - it would get triggered whenever
anyone used Bio.SeqRecord
Would anyone object if we removed Bio.FormatIO (and its hooks in
Bio/SeqRecord.py and Bio/Search.py) entirely for the next release?
Speak now or forever hold your peace! ;)
Peter
Peter wrote:
> With the release Biopython 1.43 and Bio.SeqIO earlier this year, would
> anyone be upset if the older Bio.FormatIO module was marked as
> deprecated for the next Biopython release?
>
> This module isn't mentioned in the tutorial/cookbook, but Brad did write
> this entire document:
> http://www.biopython.org/DIST/docs/cookbook/genbank_to_fasta.pdf
> http://www.biopython.org/DIST/docs/cookbook/genbank_to_fasta.html
>
> In addition to marking Bio.FormatIO as deprecated, I would probably add
> a big disclaimer to that document, or re-write it to use Bio.SeqIO instead.
>
> Thanks
>
> Peter
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