Julia syntax in vim

I try to put julia syntax in Macvim. I found this github repository: https://github.com/JuliaEditorSupport/julia-vim and I blindly follow the instructions in https://github.com/JuliaEditorSupport/julia-vim#manually , starting from ~/.vim . It does work:

There are some cool tricks, for instance I can write Unicode :
\alpha + Tab = α

tests with Julia

So, after having installed Julia months ago I gave it some tries. The speedup seems larger than an order of magnitude in both cases

looping through the same matrix

R

system.time({val=0; for (i in 1:2000){for (j in 1:2000){val=val+a[i,j]}}; val})
   user  system elapsed 
  1.862   0.015   1.868 

Julia

julia> tic(); val=0; for i in 1:2000; for j in 1:2000; val=val+a[i,j]; end; end; println(val); toc()
5.142821063269366
elapsed time: 0.327145074 seconds
0.327145074




Singular value decomposition of a 2000 x 2000 matrix

> a=matrix(rnorm(4000000),2000)
> system.time(svd(a))
   user  system elapsed 
 27.419   0.218  27.452 

Julia

julia> tic(); a=randn(2000,2000); toc()
elapsed time: 0.673701438 seconds
0.673701438

julia> tic(); svd(a); toc()
elapsed time: 5.236212822 seconds
5.236212822

transposing marker data

Quite frequently one may find marker data ordered in this way:

alegarra@genotoul2 ~/save/progs $ cat ex_rachel

 1 a b

 1 b b

 1 c c

 2 b b

 2 c c

 2 d d

 3 a b

 3 b b

 3 c c

e.g. there are three animals (1 to 3) and three markers. Rachel and I would like them to be formatted one animal per line and markers one after each other, in this way:

alegarra@genotoul2 ~/save/progs $ cat out

         1 ab bb cc 

         2 bb cc dd 

         3 ab bb cc 

This is conceptually simple if animals are sorted:

1. Read a line
2. If the animal is the same as the old one, print the markers after the previous one
3. If the animal is different, start a new line, print the animal and the markers.
4. Add special cases for the first and last line

Here is an awk implementation

alegarra@genotoul2 ~/save/progs $ cat SNPcol2line.awk 

#! /bin/awk -f

# this program reads genotypes in one line per locus

# then puts them as

# individual allele1 allele2 allele1 allele 2

#

BEGIN{

idold=0

i=0

}

{

id=$1

# if new animal

if(id!=idold){

if(idold!=0){

# close previous line

printf("\n")

}

# write new id

printf("%10s%1s",id," ")

idold=id

}

printf("%1s%1s%1s",$2,$3," ")

}

END{

# last individual

printf("\n")

}

which works:

alegarra@genotoul2 ~/save/progs $ ./SNPcol2line.awk ex_rachel 

         1 ab bb cc 

         2 bb cc dd 

         3 ab bb cc 

Sires in validation and Sires in training

I want to test metafounders for genomic selection. So I have these MTR sires that have daughters in the validation , in the training, or in both of them, and I want a file with these numbers. I have two files:

T is:
juan 10
pepe 5

V is:

luis 6
pepe 4

so luis has no daughters on Training, and I want this to appear. Then I use this pipeline from Toni Reverter from CSIRO:

awk '{print $1}' $1 $2 | sort -u | join -a1 - $1 | awk '{print $1, (NF==2?$2:0)}' | join -a1 - $2 | awk '{print $1, $2, (NF==3?$3:0)}'

which gives

putterri:yarp andres$ ./joinToni.sh V T

juan 0 10

luis 6 0

pepe 4 5

Install GNU coreutils in the Mac

The MacOSX join is poorer than GNU one. So I try toinstall it using macports. First I have to update the data base of port:

putterri:mf andres$ port -v selfupdate

But this does not work. Then I try

putterri:mf andres$ sudo port -d selfupdate

This does work. Join is actually part of coreutils:

putterri:mf andres$ port search --name coreutils

coreutils @8.25 (sysutils)

    GNU File, Shell, and Text utilities

xml-coreutils @0.8.1_1 (textproc, xml)

    Command line tools for XML processing

Found 2 ports.

So I do install coreutils:

putterri:mf andres$ sudo port install coreutils

The most important information is at the end:

The tools provided by GNU coreutils are prefixed with the character 'g' by default to distinguish them from the BSD commands.

For example, cp becomes gcp and ls becomes gls.

If you want to use the GNU tools by default, add this directory to the front of your PATH environment variable:

    /opt/local/libexec/gnubin/

Plotting correlations

I found this nice R package to plot correlations : corrplot . Imagine that you want to present five genetic correlations to your buddies. Here's how to visualize them nicely.

#create a covariance matrix
set.seed(1234)
V=rWishart(1,10,diag(5))[,,1]
cov2cor(V)
            [,1]       [,2]       [,3]       [,4]        [,5]
[1,]  1.00000000  0.1169636  0.2236465 -0.2667448  0.04351447
[2,]  0.11696358  1.0000000 -0.2260988 -0.3425368  0.64837326
[3,]  0.22364648 -0.2260988  1.0000000 -0.1883763 -0.22484960
[4,] -0.26674477 -0.3425368 -0.1883763  1.0000000 -0.50315007
[5,]  0.04351447  0.6483733 -0.2248496 -0.5031501  1.00000000
#give it names
colnames(V)=c("MY","gain","longevity","SCS","pietin")
rownames(V)=c("MY","gain","longevity","SCS","pietin")

#plot
require(corrplot)
corrplot.mixed(cor(V),col=gray.colors(10))

French Keyboard on US Macbook Keyboard

I have a US-like keyboard with this key disposition


However, it happens to me to write in French changing keyboard preferences to French. The keys are mapped to a French keyboard.  I use a rubber cover from kbcovers.com, which is excellent and looks like this:


However, the physical layout of a true French macbok keyboard is slightly different. Also, and more impostant, some important characters such as | ~ # [ ] { } are not present, or difficult to see, in the cover.

So, I prepared my own cheatsheet:


Yes, it does look horrible and yes, it does work :-)