[Biopython-dev] KEGG enhancements

[Peter Cock]

On Tue, Feb 5, 2013 at 12:32 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> Hi all,
>
> We have a couple of new pull requests for KEGG enhancements,
> which we can look at after the imminent Biopython 1.61 release
> goes out this week.
>
> Kevin's working on the REST API,
> https://github.com/biopython/biopython/pull/152
>
> Leighton's working on KGML and graphics,

Sorry, the correct URL, https://github.com/biopython/biopython/pull/155

Details below,

Peter

---------- Forwarded message ----------
From: Leighton Pritchard <notifications at github.com>
Date: Tue, Feb 5, 2013 at 12:28 PM
Subject: [biopython] KGML files (#155)
To: biopython/biopython <biopython at noreply.github.com>


As we discussed - not an ideal pull request (rebasing added the recent
Biopython changes to the KEGG branch, rather than what was expected),
but if it's workable, here's the code in a way that doesn't seem to
break Biopython ;)

L.

________________________________

You can merge this Pull Request by running

  git pull https://github.com/widdowquinn/biopython kegg

Or view, comment on, or merge it at:

  https://github.com/biopython/biopython/pull/155

Commit Summary

First addition of KGML module (with tests)
Moved Bio.KGML to Bio.KEGG.KGML and split KGML tests
Modified comments to indicate TODO
Removed accidentally-committed files
Fix typo in error message
Fix typo in blastall wrapper
Add new Blast 2.2.27+ arguments to wrappers
Ignore new blastx arguments if testing with old BLAST+
BLAST 2.2.27+ dropped -frame_shift_penalty argument
Remove deprecated Bio.File.StringHandle and SGMLStripper
Remove centre setters, add explicit deprecation warning to getters.
Clarify docstrings of deprecated BLAST functions.
Avoid ResourceWarning: unclosed file in these doctests
Close handle in this doctest
Remove the deprecated Seq object's data property
Remove duplicated section labels in Tutorial (in repeated Motifs text)
Downgrade Bio.Motif chapter to a section at the end of the Bio.motifs chapter
Fix a typo
Clarify docstring for obsolete Bio.Motif module
Explain Bio.motifs replaces Bio.Motif in its docstring
Update date in Tutorial
Fix 2 typos.
Add links to SearchIO tutorial files
Update SearchIO tutorial language style
Add links to SearchIO documentation pages
Tutorial specific example files have previously gone under Doc/examples
Update paths in tutorial after moving example files

File Changes

M Bio/Blast/Applications.py (36)
M Bio/Blast/NCBIStandalone.py (21)
M Bio/File.py (65)
M Bio/Graphics/GenomeDiagram/_AbstractDrawer.py (30)
M Bio/Graphics/GenomeDiagram/_Graph.py (14)
A Bio/Graphics/KGML_vis.py (422)
A Bio/KEGG/KGML/KGML_parser.py (184)
A Bio/KEGG/KGML/KGML_pathway.py (766)
A Bio/KEGG/KGML/KGML_scrape.py (109)
A Bio/KEGG/KGML/__init__.py (15)
M Bio/Motif/__init__.py (13)
M Bio/ParserSupport.py (34)
M Bio/Seq.py (33)
M Bio/SeqIO/SffIO.py (1)
M Bio/SeqRecord.py (6)
M Bio/motifs/__init__.py (7)
M DEPRECATED (8)
M Doc/Tutorial.tex (164)
A Doc/examples/my_blast.xml (0)
A Doc/examples/my_blat.psl (0)
A Tests/KEGG/ko01100.kgml (17805)
A Tests/KEGG/ko01100.xml (25176)
A Tests/KEGG/ko01100_mod_original.pdf (98)
A Tests/KEGG/ko01100_original.pdf (98)
A Tests/KEGG/ko01120.xml (11425)
A Tests/KEGG/ko03070.kgml (249)
A Tests/KEGG/ko03070.xml (413)
A Tests/KEGG/ko03070_mod_original.pdf (113)
A Tests/KEGG/ko03070_original.pdf (113)
A Tests/KEGG/map01100.png (0)
A Tests/KEGG/map03070.png (0)
D Tests/Tutorial/README.txt (9)
M Tests/test_File.py (13)
A Tests/test_KGML_graphics.py (138)
A Tests/test_KGML_nographics.py (99)
A Tests/test_KGML_online.py (68)
M Tests/test_NCBI_BLAST_tools.py (9)
M Tests/test_ParserSupport.py (9)
M setup.py (1)

Patch Links:

https://github.com/biopython/biopython/pull/155.patch
https://github.com/biopython/biopython/pull/155.diff