[Biopython-dev] Deprecating Bio.PDB.PSEA

[Peter Cock]

Do you know if anyone tried getting p-sea to work
on Linux (or Windows)? Right now it only seems
to work on proper Unix including macOS, which
is unfortunate.

Peter

On Thu, Jul 27, 2017 at 6:41 PM, João Rodrigues
<j.p.g.l.m.rodrigues at gmail.com> wrote:
> I'm partially against it.
>
> NACCESS is also old software, not updated since forever. This shouldn't be a
> reason for deprecating modules. If the code isn't available anymore, it's
> OK, otherwise, people might still use it. I'd send an email to the general
> users list asking first.
>
>
> A qui, 27/07/2017, 16:08, Peter Cock <p.j.a.cock at googlemail.com> escreveu:
>>
>> Thanks Patrick,
>>
>> Sourav - If there are no objections, then next week I suggest
>> you make a pull request to do the deprecation.
>>
>> Regards,
>>
>> Peter
>>
>> On Thu, Jul 27, 2017 at 3:30 PM, Patrick Kunzmann
>> <padix.kleber at gmail.com> wrote:
>> > There are also no objections from my side. If the algorithm is well
>> > documented and implementation using numpy arrays is feasible, I might
>> > integrate it in my onging develoment of a new structure subpackage.
>> >
>> > Best regards,
>> >
>> > Patrick
>> >
>> >
>> >
>> > On 27.07.2017 10:50, Peter Cock wrote:
>> >>
>> >> This came up in discussion on this pull request:
>> >>
>> >> https://github.com/biopython/biopython/pull/1336
>> >>
>> >> Quoting the tool's README file,
>> >>
>> >> "P-SEA is small tool for secondary structure assignment
>> >> from Ca cartesian coordinates of proteins. It reads
>> >> PDB-formatted file and return a file containing : the
>> >> sequence read in one-letter code and the secondary
>> >> structure assigned (a=helix, b=strand, c=coil)."
>> >>
>> >> It does compile fine on macOS Sierra, and the readme
>> >> talks about other Unix platforms (HP-UX and IRIX),
>> >> but it does not compile as is on Linux.
>> >>
>> >> In either case you get warnings about using the "gets"
>> >> function which is not secure.
>> >>
>> >> I favour deprecating Bio.PDB.PSEA
>> >>
>> >> Peter
>> >>
>> >>
>> >> On Wed, Jul 26, 2017 at 7:13 PM, Sourav Singh
>> >> <ssouravsingh12 at gmail.com>
>> >> wrote:
>> >>>
>> >>> Hello,
>> >>>
>> >>> As referenced in the subject, I would like to discuss about
>> >>> deprecating
>> >>> Bio.PDB.PSEA
>> >>>
>> >>> As referenced in the link here-
>> >>>
>> >>> ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/P-SEA.tar.gz
>> >>>
>> >>> The last update to the P-SEA package was done in September 1996, which
>> >>> makes
>> >>> it really old. I would like to know if the dev community is fine with
>> >>> deprecating the module for future releases of Biopython.
>> >>>
>> >>> Regards,
>> >>>
>> >>> Sourav
>> >>>
>> >>> Sent from my Phone.Excuse any mistakes and brevity.
>> >>>
>> >>> _______________________________________________
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>> >>
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>> >
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