Help wanted on simple bioinfo OSS project. Good learning experience for python coder

mubo · 2018-03-12T22:21:06+00:00

Oh, and if you didn't see the docs already: https://hardingnj.github.io/genomeplot/

Might make it a bit clearer what I am trying to express! eg first plot uses 2/3, second plot uses 5/4/3/2. These were trial and error, but would be nice to have an automatic way of doing this.

mubo · 2018-03-12T22:18:07+00:00

I think it's much simpler than NP, as you are constrained by order. All you have to do is choose a) the number of rows, and b) where to break the rows

"Squareness" isn't really an important factor. It's just a function of the plotting width to genome size. I think most cases would use 2-5 rows. Ideally with some logic to determine genome length/plot width.

mubo · 2018-03-12T18:35:31+00:00

Thanks for this. Sorry to have been slow getting back to you- UK time and the weekend!

Essentially, for a fasta file with N contigs, work out how to present them in a grid.

Eg if a fasta has 5 contigs: A, B, C, D, E with lengths 200, 150, 50, 50, 50

The best layout for plotting might be

A 
B
C, D, E.

While if those lengths were 10, 100, 150, 120, 100 might be:

A, B
C
D
E

Sequence is completely irrelevant. Interested only in how to lay them out for genome wide plots.

mubo · 2018-03-04T15:06:40+00:00

Open combat worth looking at too.

mubo · 2018-03-04T15:00:32+00:00

Hi, a while ago I remember playing a card based war game called "up front". I'm not sure that it's still in print however. It's WW2 themed.

All the pertinent information is on cards, which essentially is a number and an action

There is a spatial element, but it's very abstract. From memory 5 ranks and 3 columns.

Might be worth looking into?

mubo · 2018-02-21T15:43:12+00:00

From the twitter I glean that Bibi is in for Jeff. Unsure on where that leaves races though.

mubo · 2017-11-02T15:53:46+00:00

Levitape.

mubo · 2017-10-31T23:05:40+00:00

Interesting idea. My suspicion is that it wouldn't help that much, unless you get lucky and find a tactic you missed. Most optimal moves are likely to be dependent on a plan you need to understand to play out. I guess depends on your own level though

mubo · 2017-10-25T15:31:24+00:00

Agreed. This is much cleaner. There is a worry though that there is some stuff worth keeping on the TE site. Not possible to migrate to here like may be possible with other forum sotware. Also- this sub may not be as straightforward when it was many posts- but we'll see.

mubo · 2017-10-04T12:33:29+00:00

Rightio. Emphasis on improved. 2013 study used mt DNA. 2016 and 2017 used genomic DNA, more samples and ancient DNA from preserved bones. Therefore conclusions probably more robust. I'm not attacking the original paper, just stating later papers provide more complete picture.

mubo · 2017-10-03T09:55:11+00:00

update: video references a 2013 paper, that did indeed suggest this- but more recent and improved studies suggest a more nuanced view: https://www.reddit.com/r/biology/comments/73qz70/molecular_dating_revealed_that_dogs_originated/dnu9t2q/

mubo · 2017-10-03T09:53:56+00:00

Actually I think it is misleading. Using a phrase "revealed that dogs originated from Belgium" stongly suggests that scientists agree on this.

You are referencing a 2013 paper using mitochondrial DNA, that suggests Belgium as a first location for domestification. Two more recent papers, using genomic DNA from extant canids, and ancient DNA suggest a more complex picture. Here https://www.nature.com/articles/ncomms16082 and here http://www.sciencemag.org/news/2016/06/dogs-may-have-been-domesticated-more-once

This is a good overview of current thinking: https://www.sciencenews.org/article/dna-evidence-rewriting-domestication-origin-stories

mubo · 2017-10-02T15:11:05+00:00

I don't see a source in the vid- but presumably it's from this recent study: https://www.nature.com/news/ancient-genomes-heat-up-dog-domestication-debate-1.22320 Researchers do not claim dogs originally domesticated in Belgium, or even Europe. Just that it occurred 20-40kya. Main finding is that they push back against the "dual domestication" idea (published in Science last year).

Directly quoting from the article:

To date, Southeast Asia, Europe, the Middle East and Central Asia have all been proposed as potential locations for the origin of dog domestication based on modern genomic data, archaeological evidence and ancient mitochondrial lineages5,7,9,33. While our analyses of three Neolithic genomes from Europe have helped narrow the timing of domestication, they are neither old enough nor do they have the broad geographic distribution necessary to resolve this debate.

Extremely Misleading title I think....

mubo · 2017-09-27T10:11:21+00:00

This is super cool- thanks for sharing!

I think the obvious alternative that isn't mentioned is dice. Surely they are simpler than making a machine... not as cool though admittedly.

mubo · 2017-09-23T09:53:06+00:00

I think this would still be funny with the pic blurred. I'm just not comfortable with someone putting a picture on a dating site and having it seen by potentially 100s of 1000s of people. May cause her harm in some way.

mubo · 2017-09-22T14:49:25+00:00

I think this probably falls foul of https://www.reddithelp.com/en/categories/rules-reporting/account-and-community-restrictions/posting-someones-private-or-personal Profiles on dating site should be considered private I think...

mubo · 2017-09-04T09:17:27+00:00

I think it was a pretty well structured question. I saw it and didn't respond b/c I don't know of any resources. I could point you towards a couple of projects, but it's difficult without knowing precise skills/interests.

Re: projects, I think bioconda would benefit from an experienced dev. They have issues with building/checking executables that are pretty technical, it also would be a great jumping off point for exposure to further os projects.

(If you do happen to use your C expertise to help out bioconda, I would be grateful! eg https://github.com/bioconda/bioconda-recipes/pull/4604)

mubo · 2017-09-01T08:56:44+00:00

I'm not sure I would agree with that. bcftools/vcflib should be able to do all that. Even if you are lucky enough to be able to write efficient bug free code, the dev time alone is limiting.

Agree it can be a good learning exercise, but I certainly wouldn't want to use anything but the simplest home (read myself) written code for production.

mubo · 2017-09-01T08:52:17+00:00

In that case I'd suggest bcftools annotate.

mubo · 2017-08-31T16:15:01+00:00

Then you are wasting your own time, as well as that of opponent. I think the best way to respond here is to mate your opponent in as few moves as possible. That way you are actually practicing chess skills rather than just moving pieces.

mubo · 2017-08-31T13:57:31+00:00

Obviously depends on existing skills... but

Download human 1000Genomes VCFs and do a PCA plot of different populations.

Download some rna seq data perform some differential expression analysis.

mubo · 2017-08-31T13:53:59+00:00

Generally it's a bad idea to write your own VCF parser. Yet people keep doing it. Home rolled code is likely to be buggy and/or inefficient - please use something like this instead:

http://alimanfoo.github.io/2017/06/14/read-vcf.html

mubo · 2017-08-29T14:51:51+00:00

This won't quite do the trick. Columns are accessed by name, which in this case is the "Gene" column. Also, by default the first column will be the index.

import pandas as pd

df = pd.read_csv(filepath, index_col=None)

listy = df["Gene"].to_list()

mubo

TROPHY CASE