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Spencer Bliven
@sbliven
@abhinavprince #206 is a useful one ;)
end shameless plug
Alex G Rice
@guidorice
Hi @wilzbach , I have run into some trouble with the Sequence Logo. I think this might be some kind of css conflict or canvas rendering problem- not sure. What it looks like is just an empty white area where the logo should be.
msa.png
In the chrome inspector, I see the dom elements - div.logo_container div..logo_graphic, canvas.canvas_logo.
I have no idea why the logo is empty white space, and there are no javascript errors or warnings.
I tried loading the same data file into an empty page with only the msa component, and in that case the logo appeared OK.
But I am pretty stumped how to debug this. Using version 1.0 from your cdn.
All the dom elements seem to be sized OK and in the right place.
Alex G Rice
@guidorice
Is there a way to force the canvas to redraw for the seqlogo?
Alex G Rice
@guidorice
@emepyc @wilzbach and everyone: we went live today with a part of our site using the tnt.tree and the msa components from biojs project. An example gene family: http://legumeinfo.org/chado_phylotree/phytozome_10_2.59033656 or search/browse the index at http://legumeinfo.org/search/phylotree Thanks for making such cool javascript components, couldnt have done it without you.
Carlos Henrique
@carlosmr12

Hello everyone, I was wondering if there is a way to highlight a few residues in each of the sequences in the viewere. Something like this http://kin-driver.leloir.org.ar/msa.php?uniprot=EGFR_HUMAN/712-968&mutation=G719A .

The idea is basically the same of the link above, highlight mutated residues in each sequence and after that implement the "hover residue".

Also I was wondering if there is any information on the sequence logo that I could extract programatically, like for example in the position 346 there is a Asp in 34% of sequences and a Tyr in 66% of sequences. (Not sure if that is possible, but I could always implement a python script for calculating that information, but perhaps it is already there somewhere that I could not find) :)

Spencer Bliven
@sbliven
@carlosmr12 I'm not sure if this is the most efficient way to color some residues, but you could use a custom colorscheme
something like (untested):
msa.g.colorscheme.addDynScheme("custom_scheme",function(letter,opts){if( opts.x == 4 && opts.y == 0){return "#f00";} else {return "#fff";}})
msa.g.colorscheme.set("scheme","custom_scheme")
I'm not sure what you want to do with hovers, but be aware there's an outstanding bug on that issue (#206)
elilk
@elilk

We are looking for a mechanism that will allow us to color the whole column by a specific color.
For example, if column 1 has score X it will be colored in Y.

Currently, we achieve this by coding the MSA into an HTML with styles (which is inefficient for large alignments). e.g.:
alt

Ideally, we could replace this HTML coloring with your tool. Is there such an option?

Thanks!

Carlos Henrique
@carlosmr12

@sbliven Thanks. I will let you know if that works.

The hover thing it would just be a bonus, but I also check that issu, thanks for the advice.

Spencer Bliven
@sbliven
@elilk Do you need custom column scores? I think there is a built-in scheme based on conservation, or you can use a dynamic color scheme for more control. See my previous comment, or https://github.com/wilzbach/msa-colorschemes for details.
How many sequences are do you need? I haven't used MSA for big alignments myself, but if you're running into problems with rendering pure HTML then you might also run into problems with javascript. Maybe you can load sequences progressively as the user scrolls down, or use some clustering? I doubt users really want to see thousands of rows.
quorak
@quorak
hey there.
greate plugin, this really eases my life.
we just finished writing our Secondary Structure Predictor and have different likelyhoods for H C E Structures. I would like to show them with MSA and thought about adjusting the heights of the sequence logos.
quorak
@quorak
But i could not realy find a way to inject our values into here https://github.com/wilzbach/msa/blob/master/src/views/header/SeqLogoWrapper.js
anybody any idea ?
xiuFeng
@whoKnowsss
Hi, the demo only shows 15 lines , i'd like to expand it to show more lines. What should i do...Thx~~
Noirot CĂ©line
@noirot
Hi!
I use msa with the function importURL, but it add before my url : https://cors-anywhere.herokuapp.com/, does it normal ???
Daniel
@DanBuchan

Hi,

When loading a new instance of the MSA viewer how do I import both a new MSA and a set of annotations?

The example you provide only shows getting an alignment at launch/render
m.u.file.importURL("http://rostlab.org/~goldberg/jalv_example.clustal", function(){
m.render();
});

Daniel
@DanBuchan
I also have the https://cors-anywhere.herokuapp.com/ problem
Daniel
@DanBuchan
@noirot consider using the msa.io.fasta.read() and msa.io.clustal.read() functions to work around that herokuapp url problem
pterzian
@pterzian
Hey there!
Is there a way to download the actual msa.min.js instead of sourcing it from the web everytime?
cheers
Sebastian Wilzbach
@wilzbach
Sorry that I haven't been active on gitter recently
@pterzian s http://cdn.bio.sh.s3.eu-central-1.amazonaws.com/msa/latest/msa.min.gz.js
@DanBuchan @noirot yeah, that's normal as CORS is required for importing URLS from servers which don't support it. You can always roll your own cors proxy by modifying
g.conf.importProxy
erlog
@erlog
Hello, I'm part of a project that does very large MSA's, but MSA viewer crashes for me in Chrome when we have about 50k sequences. Is there any work that will be done on performance?
pterzian
@pterzian
Hi guys,
I would like to put the overview pannel in a div with predefined size, so it fit my webpage in the case of big MSAs when I display it. Any idea about where to start ?
many cheers
Andy S
@andyS2018_gitlab
Hi Guys, What is the best way to highlight some region of interest using MSA JS library? Is there example that you can share? Thanks in advance.
uhilgert
@uhilgert
Cool tool! We integrated it into DNA Subway's (dnasubway.org) Yellow Line and it works like a charm. Takes only a little tweaking to set up Chrome adequately, if exporting to JalView is desired, but nothing that can't be solved. Question: will the imminent changes concerning the Java browser plugin affect MSA?
puhuangwustl
@puhuangwustl
Hey there!
Is there a way to make exported fasta be compatible with windows new line '\r\n'? Under windows text viewers the default new line sign '\n' could not be recognized. Thanks!
Eduardo
@esanzgar
Is there any global event that I can listen to inform when the viewer has been rendered? I would like to have some kind of loading bar or spinner while waiting.
Eduardo
@esanzgar
EMBL EBI workspace.png
Does anybody knows how to get rid of this extra space?
Eduardo
@esanzgar
EMBL EBI workspace (1).png
It seems that the extra space only happens when there are few sequences
Peter Rose
@pwrose
Is there a Python wrapper for MSA so it can be used in Jupyter Notebooks?
Sebastian Wilzbach
@wilzbach
/all I'm working with Plotly to release a new MSAViewer soon. It's written up from scratch with many of the shortcomings of the current viewer in mind. It will use the MIT license and will be compatible with Dash.
More infos: https://github.com/plotly/react-msa-viewer (it's still WIP for now)
@pwrose You'll be able to use the new MSAViewer with Jupyter Notebooks directly via Dash.
Spencer Bliven
@sbliven
@wilzbach Exciting!
kchennen
@kchennen
Hi @esanzgar. I would like to know if your version of the MSA with possibility to edit selecting/grouping sequences and editing the alignment will be available for the community?
Peter Rose
@pwrose
Could you have a look at: wilzbach/msa#226. This blocks usage in Jupyterlab.
Sebastian Falk
@TheBrainOfPinky_twitter
The App https://msa.biojs.net/app/ is not. loading. I have tried various browser but nothing is happening there. Any recommendations?
Spencer Bliven
@sbliven
@TheBrainOfPinky_twitter It's an SSL problem. http://msa.biojs.net/app/ works fine.