[Biopython-dev] Releasing (a beta of) Biopython 1.62 this week?

Wibowo Arindrarto w.arindrarto at gmail.com
Sat Jul 13 06:58:23 UTC 2013

Hi Michiel,

There are two classes from Bio.Blast.NCBIStandalone still being used
by Bio.SearchIO internally (for the BLAST text parser): the
BlastParser and the Iterator classes. The BlastParser class itself
still relies on Bio.ParserSupport. Would it be ok if we move parts
that are used by SearchIO into their own private classes in
Bio.SearchIO, while putting the BiopythonDeprecationWarning on the
current files?

Best regards,

On Sat, Jul 13, 2013 at 3:52 AM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> The following pieces of code had a PendingDeprecationWarning in Biopython release 1.61, and can be upgraded to a BiopythonDeprecationWarning:
> Bio.Blast.NCBIStandalone (entire module). This module has had a PendingDeprecationWarning since September 2010.
> Bio.Motif (entire module). Its functionality is available from Bio.motifs, so Bio.Motif can be deprecated.
> Bio.ParserSupport (entire module). This module is currently only being used by Bio.Blast.NCBIStandalone, and has had a PendingDeprecationWarning since September 2011.
> Any final objections?
> Best,
> -Michiel
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