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- biopython/DEPRECATED modified
revision 1.42
date: 2009/01/04 22:00:39; author: peterc; state: Exp; lines: +14 -12
Centre/center in GenomeDiagram
- biopython/Bio/SeqRecord.py modified
revision 1.27
date: 2009/01/03 13:22:07; author: peterc; state: Exp; lines: +8 -3
Using StringIO's getvalue method in format methods and tutorial.
Adding some missing copyright/license text.
Minor additions to the Entrez chapter of the tutorial.
- biopython/Bio/Align/Generic.py modified
revision 1.17
date: 2009/01/05 17:52:29; author: peterc; state: Exp; lines: +11 -11
Fixed an alphabet abuse in the doctests (invalid letter D used)
- biopython/Bio/Blast/NCBIWWW.py modified
revision 1.56
date: 2009/01/02 23:18:01; author: peterc; state: Exp; lines: +29 -6
Further tweaks to the error handling for RTOE and RID, to try and be more helpful
when something goes wrong.
- biopython/Bio/Graphics/BasicChromosome.py modified
revision 1.3
date: 2008/12/23 13:09:47; author: peterc; state: Exp; lines: +3 -2
ReportLab's writeToFile functions and Canvas object will take either a filename or a handle. Updating our docstrings to clarify that our write-to-file methods will also take handles (Bug 2718).
- biopython/Bio/Graphics/Comparative.py modified
revision 1.2
date: 2008/12/23 13:09:47; author: peterc; state: Exp; lines: +7 -0
ReportLab's writeToFile functions and Canvas object will take either a filename or a handle. Updating our docstrings to clarify that our write-to-file methods will also take handles (Bug 2718).
- biopython/Bio/Graphics/Distribution.py modified
revision 1.3
date: 2008/12/23 13:09:47; author: peterc; state: Exp; lines: +2 -1
ReportLab's writeToFile functions and Canvas object will take either a filename or a handle. Updating our docstrings to clarify that our write-to-file methods will also take handles (Bug 2718).
- biopython/Bio/Graphics/GenomeDiagram/AbstractDrawer.py modified
revision 1.7
date: 2009/01/04 21:56:47; author: peterc; state: Exp; lines: +17 -5
Switching from UK spelling centre to US spelling center, while attempting to preserve
backwards compatibility. See also the earlier colour/color changes in the spirit.
- biopython/Bio/Graphics/GenomeDiagram/CircularDrawer.py modified
revision 1.11
date: 2009/01/04 21:56:47; author: peterc; state: Exp; lines: +54 -53
Switching from UK spelling centre to US spelling center, while attempting to preserve
backwards compatibility. See also the earlier colour/color changes in the spirit.
- biopython/Bio/Graphics/GenomeDiagram/Diagram.py modified
revision 1.4
date: 2009/01/05 23:16:24; author: peterc; state: Exp; lines: +35 -49
Given ReportLab uses a StringIO handle for its writeToString method,
we'll do the same in order to simplify our code (see Bug 2711).
Also allow format names in any case (see Bug 2718).
- biopython/Bio/Graphics/GenomeDiagram/Graph.py modified
revision 1.3
date: 2009/01/04 21:56:47; author: peterc; state: Exp; lines: +14 -2
Switching from UK spelling centre to US spelling center, while attempting to preserve
backwards compatibility. See also the earlier colour/color changes in the spirit.
- biopython/Bio/Graphics/GenomeDiagram/GraphSet.py modified
revision 1.3
date: 2009/01/04 21:56:47; author: peterc; state: Exp; lines: +9 -5
Switching from UK spelling centre to US spelling center, while attempting to preserve
backwards compatibility. See also the earlier colour/color changes in the spirit.
- biopython/Bio/Graphics/GenomeDiagram/LinearDrawer.py modified
revision 1.8
date: 2009/01/04 21:56:47; author: peterc; state: Exp; lines: +21 -20
Switching from UK spelling centre to US spelling center, while attempting to preserve
backwards compatibility. See also the earlier colour/color changes in the spirit.
- biopython/Bio/KEGG/Compound/__init__.py modified
revision 1.10
date: 2008/12/31 17:13:24; author: peterc; state: Exp; lines: +42 -1
Adding a simple doctest to the Bio.KEGG.Compound docstrings.
- biopython/Bio/KEGG/Enzyme/__init__.py modified
revision 1.11
date: 2009/01/01 20:32:10; author: peterc; state: Exp; lines: +41 -0
Adding basic doctest to Bio.KEGG.Enzyme parse function.
- biopython/Bio/Sequencing/Phd.py modified
revision 1.17
date: 2008/12/22 17:10:28; author: peterc; state: Exp; lines: +3 -4
Don't use the IUPAC ambiguous DNA alphabet as it only allows upper case letters (see Bug 2597). If we add mixed case IUPAC alphabets, using one of those should be OK (Bug 2532)
- biopython/Doc/Tutorial.tex modified
revision 1.191
date: 2009/01/03 14:32:21; author: peterc; state: Exp; lines: +8 -7
Fixed another StringIO getvalue case, a couple of typos, etc.
- biopython/Doc/install/Installation.tex modified
revision 1.16
date: 2009/01/04 18:53:21; author: peterc; state: Exp; lines: +30 -21
Fixed a couple of broken links.
Clarified the mxTextTools situation (mentioning release 1.49).
Added a section on third party tools.
See Bug 2723.
- biopython/Tests/test_Clustalw_tool.py modified
revision 1.5
date: 2009/01/05 19:16:09; author: peterc; state: Exp; lines: +6 -8
Properly tested fix to remove DND files, after my premature previous effort
- biopython/Tests/test_GenomeDiagram.py modified
revision 1.15
date: 2009/01/05 23:18:08; author: peterc; state: Exp; lines: +8 -10
We now allow format names in any case (see Bug 2718).
Also test the draw_to_string method at least once.
- biopython/Tests/test_docstrings.py modified
revision 1.8
date: 2009/01/01 20:32:10; author: peterc; state: Exp; lines: +5 -0
Adding basic doctest to Bio.KEGG.Enzyme parse function.
- biopython/Tests/output/test_Clustalw_tool modified
revision 1.3
date: 2009/01/05 19:15:24; author: peterc; state: Exp; lines: +0 -7
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