[Biopython] Bio.PDB local MMCIF files
Michiel de Hoon
mjldehoon at yahoo.com
Sat Dec 28 02:10:24 UTC 2013
Various issues of the MMCIF parser also came up previously, see for example the thread starting here:
http://lists.open-bio.org/pipermail/biopython-dev/2013-March/010452.html
I'd like to propose to make the MMCIF parser a bit more Pythonic and more consistent with other Biopython modules.
This is a description of how the MMCIF parser would work:
http://biopython.org/DIST/docs/tutorial/Tutorial.mmcif_proposal.html#htoc149
This uses a new Bio.PDB.mmcif module that has a read() function (taking both file names and file handles) which stores the information in an MMCIF file in a mmcif.Record object, which is a Python dictionary.
Please have a look if you agree or have any comments or suggestions. If this looks OK, I can upload the new code.
Best,
-Michiel.
--------------------------------------------
On Thu, 12/5/13, Peter Cock <p.j.a.cock at googlemail.com> wrote:
Subject: Re: [Biopython] Bio.PDB local MMCIF files
To: "João Rodrigues" <anaryin at gmail.com>
Cc: "Biopython Mailing List" <biopython at lists.open-bio.org>
Date: Thursday, December 5, 2013, 12:35 PM
On Thu, Dec 5, 2013 at 4:53 PM, João
Rodrigues <anaryin at gmail.com>
wrote:
> Hi Dave,
>
> I understand your concern. Python has the gzip module
that can decompress
> the files on the file and provide a handle for the
content. This will not
> work for the parsers since they except a filename. I
will have a look at
> the parsers code and if it's simple, I'll add a layer
to do this exactly.
>
> Cheers,
>
> João
Yeah, most of Biopython's parsers take a handle only, some
like the top level functions in Bio.SeqIO, AlignIO,
SearchIO
will take a filename or a handle for convenience.
I agree that is is unfortunate that Bio.PDB currently only
takes
a filename (historical design choice). If we can tweak it to
take
either a filename or a handle that would be much better :)
Regards,
Peter
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