Mystery Rays from Outer Space

After spending a week¹ trying to find a bug in XPlasMap, I just realized that “[-\d]+” should have been “[-\d\.]+”

Sheesh.

1. Well, a half-hour every other night for a week[↩]

In case anyone cares, I’m still slowly¹ working on making a non-beta version of XPlasMap. (The present release is 0.96 [see comments here], so it’s getting incrementally closer to 1.0.) I’ve squashed a few bugs, and added a few features, but much of what I’ve been doing has been kind of shuffling things behind to scenes to make it a little easier to maintain, and also to prepare for adding a couple of features that would have stepped on the toes of the original setup.

I spent the morning trying to figure out why printing was suddenly low-resolution, a bug I thought I had fixed several iterations ago. Turns out the fix only works with the most recent versions of wxPython, whereas I was still working with the builtin 2.8.4.0 in the hope of making the file more portable on Leopard. There’s nothing in the release notes that I can see, but when I switched back to 2.8.7.1 print resolution was back to the proper level again.

There are a couple of things in the ToDos that probably won’t make it into v. 1.0, but most of them should, I think.

XPlasMap ToDos for v 1.0

• BUG - Clicking on anything often selects the plasmid rather than the feature itself. (Take the plasmid out of the pathlist)
• BUG - Changing gene text parameters overrides text position
• BUG - Fix highlights in Cut Dialog
• BUG - Split MCS doesn’t work with no downstream sequence/site
• BUG - Hide/show text in List View is really slow for a batch of genes!
• BUG - writeXMLFile intermittently throws error at self.recentFilesMenu.Delete(deleteId) - “invalid item in wxMenu.Delete”
• BUG - Show/hide comment contextual menu doesn’t work
• BUG - When importing from FastA make sure first save prompts for a name
• “Info” icon in toolbar
• Highlight features when selected
• Flip text orientation manually
• Insert fragments by restriction site
• More fine-grained control of fonts
• Determine PNG and JPG resolution at export time
• When importing and identifying sequences, put enzyme sequence into “Note”
• When opening a file, put MCS center (etc) in if missing. Also put in during creation in dialog
• Convert restriction sites to MCS
• Magnifying-glass-type zoom
• Error message if “Import” tries to open an incorrect file type
• Checkbox - Identify ORFs in Genbank imports (Default on or off in preferences)
• Annotation menu
• Add special symbols for Annotations (Arrows, brace-brackets, etc)
• Status bar - show mouse position in nucleotides
• Speed up changes in List View
• Improve batch handling of genes
• Clean up the code for the copy and cut fragment sections
• Turn plasmid name and description into a free-standing comment
• (With special double-click characteristics?)
• Import from ApE gb files (APE gb files are broken, repair their LOCUS line spacing and then import; or write a less restrictive GenBank interpreter)
• Import from GB as circular when noted in LOCUS line
• Report error when ImportFromGB module fails
• Print from ListView
• BUG - short gene goes all the way around when crossing the 90^o point
• BUG - Printing more than one page doesn’t work (Use GetVirtualSize instead of GetSizeTuple; But this causes problems for the next page, if it’s smaller)
• BUG - Printing is low-resolution (again!)
• BUG - Highlight color is too opaque
• BUG - “No features are selected” in List View
• BUG - Text height of new import is off the window
• BUG - Short genes only show clockwise arrow
• Grab “Product” from GenBank imports for names
• Batch entry for restriction sites
• Batch entry for genes
• Change “Insert fragment” shortcut from “⌘I” to “⌘V”; change “Edit plasmid info” shortcut to “⌘I”

1. XPlasMap is lower priority than writing grants, teaching, doing lab work, and taking kids to birthday parties and tobogganing, so that leaves about an hour twice a week, late at night when the kids are asleep, for XPlasMap.[↩]

I’ve released a new version of XPlasMap, version 0.96 (asymptotically approaching a non-beta release). XPlasMap 0.96 can be downloaded here, and the XPlasMap home page is here.

XPlasMap is a DNA drawing program for MacOSX (MacOS10.4 and up only for this release; a slightly older version runs on MacOS10.3 [download XPlasMap10.3 here] ) It draws plasmid maps with all the features you’d expect (genes, multiple cloning sites, restriction sites, and so on), pretty much interactive. It also draws linear DNA maps and will draw maps by importing directly from GenBank files. It will also import from FastA files; for both FastA and GenBank sequence it will map out restriction sites (slowly! –it’s no competition for specialized restriction mapping programs like EnzymeX or the venerable DNA Strider) and identify open reading frames (again, slowly). Maps can be saved as .xpmp files (which is simply an XML format; I wanted to make sure that the information in the maps would remain accessible and in a non-proprietary format), or exported to PNG or JPG.

Here’s a sample plasmid map, for Invitrogen’s pTracerCMV2 (click on the image for a larger version):

And here’s a sample of a linear DNA map (click for a larger version). This is the human genomic major histocompatibility region, imported directly from a GenBank file (3.7 million base pairs). The class I region is highlighted in orange, class III region in green, and class II region in blue.

The 0.96 release is mainly a bug-fix release; there are preliminary versions of a couple of new features, with annotations being the main new feature.

New features:

• Annotations
• “Plasmid comment” is now free-form text (can be moved and edited)
• (Preference option) Common actions on a toolbar

Bugfixes:

• Improved print resolution
• Fixed: Intermittent Clear Recent Files bug
• Fixed: JPG and PNG exports use a large canvas with image only in one corner
• Fixed: Error on copying in reverse
• Fixed: Font preferences not always honored
• Fixed: Going from linear to circular, genes disappear
• Fixed: Contextual menus occasionally not responding
• Fixed: Show/Hide enzyme lost after save
• Fixed: Genes with no name disrupt drawing
• Fixed: Freeze in Cut Plasmid
• Fixed: Hiccup if no Preference file

Assorted other bugfixes and UI improvements

XPlasMap only runs on Macs (though it’s written in Python/wxPython, which means that it should be a straightforward recompile to run on other OSes — but I only use Macs so haven’t tried). I also wrote a much more primitive (but still rather attractive) on-line plasmid-mapping program that is OS-independent: Savage Plasmids draws SVG maps and exports to Postscript. Unfortunately browser support for SVG is still at best spotty and hasn’t improved much over the past couple of years, as far as I know.  SVG will do interactive, but I’ve never got around to making the program interactive (and likely never will, now), so XPlasMap really makes much nicer maps.