Question: Plotting Dna Sequence Traces
2
gravatar for Sabrewolfy
8.0 years ago by
Sabrewolfy80
Sabrewolfy80 wrote:

I have read/consulted these two threads here, the ABI file format document, the BioPython project, the R project, the BioConductor project and have searched extensively on the Internet, but I am not able to find an answer or explanation for what I would like to do.

<del>I would like to know how to interpret trace data from an ABI/AB1 trace file and how to plot this data. Ideally, I'd like to plot it on a web-page (in some format that allows for scrolling of course, but I haven't thought that much about this yet), but first I need to understand the trace data itself and how to plot it with Python and/or R.</del>

Edit: I have managed to extract the raw point data from chromatogram files. What approach should I take to plot curves like the trace-viewing programs do (FinchTV, Chromas, etc.) ? After much searching, I've found this and this. Are these the right approach or do I need a spline function?

python visualization biopython R • 3.4k views
ADD COMMENTlink modified 5.2 years ago by Biostar ♦♦ 20 • written 8.0 years ago by Sabrewolfy80
4
gravatar for Daniel Swan
8.0 years ago by
Daniel Swan13k
Aberdeen, UK
Daniel Swan13k wrote:

Are you sure you read to the bottom of those threads? There is a link here which would be the starting point for such an endeavour assuming you want to write your own parser for display. I still don't know why you would want to do this when a number of things will already render an ab1 file, and then you just write the HTML display 'widget' around the output of one of these.

ADD COMMENTlink written 8.0 years ago by Daniel Swan13k
2

I had read to the bottom of those threads many times. The answer you linked to was only posted yesterday :) Thanks for the link though; I'll look through the details referred to.

ADD REPLYlink written 8.0 years ago by Sabrewolfy80

Yes - I noticed that, hence I thought it was worth posting as a reply ;)

ADD REPLYlink written 8.0 years ago by Daniel Swan13k

An HTML widget would not allow the user to change the scale and scroll across the entire trace image though? I could maybe just insert an image of the abi file. abiview exports the trace as an image but the quality is not good and it exports it as several image files. Running it with parameters to use only one window yields the entire trace in one image, but of the same width as one of the pieces, so that the entire trace is squashed into 800 horizontal pixels. BioLign will export the entire trace as an image, but is Win32 and cannot be run as part of a pipeline.

ADD REPLYlink written 8.0 years ago by Sabrewolfy80

I see my question in the comment above is similar to this: http://biostar.stackexchange.com/questions/2584/please-suggest-some-command-line-tools-for-displaying-abi-trace-file-on-windows-o/

ADD REPLYlink written 8.0 years ago by Sabrewolfy80

No I imagine to do something like that you would need to write a parser that creates an SVG output rather than just displaying (for instance) the output of ABIview

ADD REPLYlink written 8.0 years ago by Daniel Swan13k
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