Author: microbe

Index fasta file generating fai file to use…

http://adsecurite.fr/?seledka=rencontre-femme-de-ma-r%C3%A9gion&8e6=35 Index fasta file – generating fai file – to use with IGV or bedtools.

samtools faidx reference.fasta
http://genomeview.org/content/preparing-fasta-files

November 26, 2012
Convert all tabs to spaces and vice versa…
Convert all tabs to spaces and vice versa.

You can use the :retab command to convert all existing tabs to spaces. You can do both in one command:
```
:set et|retab
```
You can also convert spaces to tabs:
```
:set noet|retab!
```
http://vim.wikia.com/wiki/Super_retab
November 20, 2012
Vim plugin surround Normal mode ds delete a…

Vim plugin surround

Normal mode
———–
ds – delete a surrounding
cs – change a surrounding
ys – add a surrounding
yS – add a surrounding and place the surrounded text on a new line + indent it
yss – add a surrounding to the whole line
ySs – add a surrounding to the whole line, place it on a new line + indent it
ySS – same as ySs

Visual mode
———–
s – in visual mode, add a surrounding
S – in visual mode, add a surrounding but place text on new line + indent it

http://www.catonmat.net/blog/vim-plugins-surround-vim/

November 3, 2012
http jeromyanglim blogspot ca 2010 05 abbreviations of…

http://jeromyanglim.blogspot.ca/2010/05/abbreviations-of-r-commands-explained.html

250+ R commands.
Often times R users suffer from difficulties finding what commands are available for a specific process.
This lists 250+ R commands in table.

November 2, 2012
Surround a VIM plugin that surrounds a word…

Surround, a VIM plugin that surrounds a word or a line.

http://www.catonmat.net/blog/vim-plugins-surround-vim/

August 24, 2012
Perl Getopt Long The module check wrong argument…
Perl Getopt::Long.

The module check wrong argument but does not check when no argument is provided.
In order to check if there is no argument as well as wrong argument,
check the argument also.
```
GetOptions( 'test=s' => \$option_test )
    or exit(1);

defined($option_test)
    or die("Missing argument -t");
```
http://www.perlmonks.org/?node_id=789974
August 17, 2012

Auto size of images in Beamer class \usepackage…

Auto size of images in Beamer class.

\usepackage{letltxmacro}
\makeatletter
\def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth\else\Gin@nat@width\fi}
\makeatother
\AtBeginDocument{
  \LetLtxMacro\Oldincludegraphics\includegraphics
  \renewcommand{\includegraphics}[2][]{%
    \Oldincludegraphics[#1,width=\maxwidth]{#2}}
}

http://tex.stackexchange.com/questions/67434/redefine-includegraphics-for-beamer#comment143600_67434

August 17, 2012

Beamer paper size is smaller than usual paper…
Beamer paper size is smaller than usual paper size.
The “paper size” of a beamer presentation is ﬁxed to 128mm times 96mm.

With this trick, the normal font can be shown nicely.
But be cautious setting the image size with absolute value.
or use
```
\includegraphics[width=0.6\textwidth]{graphics.pdf}
```
http://web.mit.edu/8.13/presentations/beameruserguide.pdf

Citation
August 16, 2012
R color palettes # Basic grDevice rainbow topo…
R color palettes
1. Basic grDevice
rainbow()
topo.colors()
terrain.colors()
heat.colors()
```
my.palette <- terrain.colors(100)
```
1. RColoBrewer package
```
display.brewer.all()
```
my.palette <- brewer.pal(n, name) For example, my.palette <- brewer.pal(9, "Blues") However, the number of colors is limited up to 9, in most colors. Then use this.
```
more.color.palette <- colorRampPalette(brewer.pal(9,"Blues"))(100)
```
http://stackoverflow.com/questions/3832850/color-schemes-in-r
http://www.compbiome.com/2010/12/r-using-rcolorbrewer-to-colour-your.html
August 9, 2012
RColorBrewer palette names

RColorBrewer palette names.

August 9, 2012