Stuff I Routinely Forget How to Do

I need an internet connection to program well because I'm constantly looking up things I've forgotten. Thankfully, all that information is stored in my "outboard brain" searchable by Google. I figured I'd collect the useful bits into a growing list, in the hope that others may benefit from my documented forgetfulness.

It's really a letter of advice from Past Christina to Future Christina.

Quick Links

Perl
R
Unix/bash
CSS
HPC
git

Perl

For each file in a directory

Capture a list of all files in a directory with the glob function:

@files = <*>;
@txt_files = <my_dir/*.txt>;

foreach $f (@files) {
    print $f . "\n";
}

Push items into array

Why can I never remember the order of this? It's:
```
push @array, $element;
```
Split string into array of strings

Another one I alway mess up:
```
split /PATTERN/,EXPR,LIMIT
```
Install a module with CPAN
```
perl -MCPAN -e 'install X::Y'
```

Install a module with CPAN in a non-standard location

o conf mbuildpl_arg "--install_base /path/to/perl-modules/"
o conf makepl_arg "PREFIX=/path/to/perl-modules/"
install X::Y

Quickly Create Hash of Arrays

Load the arrays in the hash without building the arrays, then dereferencing them into the hash. Found here.
```
push(@{$hash{$key}}, $insert_val);
```

R

Remove NAs from a vector
```
x[!is.na(x)]
```
Combine multiple plots in one graph
```
par(mfrow=c(num.rows, num.cols))
```
Generate the R code needed to reproduce an object
```
dput(head(iris))
```
Using Variables within expression()

See this answer on StackOverflow.
```
alpha = 0.05
bquote("Representation in Low"~F[ST]~Regions~"(p"*""<=~.(alpha)*")")
```
"The ~ is a spacing operator and * means juxtapose the contents to the left and right of the operator. In bquote(), anything wrapped in .( ) will be looked up and replaced with the value of the named object; so .(assay) will be replaced."

Create Function with Range of Possible Parameters and Default

Description can be found here. In this function, age can only be adult or subadult and defaults to adult:

my.function = function(name, age = c("adult", "subadult")) {
    ## evaluate choices
    age = match.arg(age)
    print(age)  # Defaults to adult
}

Unix/bash

Sort by date

Use the -t flag with ls to sort by date files were last modified (or -tr to sort in reverse).
```
ls -lht
```

Use process substitution

Explained a bit more here.

diff <(ls /scratch/secret_project/) <(ls /archive/secret_project/)

List files and sort numbers "naturally"

Natural sort means sorted like this:
```
chr1.fa
chr2.fa
chr10.fa
```
instead of this:
```
chr1.fa
chr10.fa
chr2.fa
```
You can do this with ls -v. Using this natural sort with xargs is super handy for cat'ing together chromosomes in order:
```
ls -v chr*.fa | xargs cat > genome.fa
```

Keyboard Shortcuts

A subset of the ones found here and here.

Combo	Action
`CTRL+S`	Stops output on screen (XOFF).
`CTRL+Q`	Turns stopped output back on (XON).
`CTRL+U`	Erases (cuts) the complete line.
`CTRL+Y`	Pastes line cut with CTRL+U.
`CTRL+W`	Deletes the last word typed. `mv file1 file2` becomes `mv file1`.
`CTRL+L`	Clears the screen, redrawing the current line.
`CTRL+G`	Abandons the current line

Recall Last Argument of Previous Command

Quickly grab the last command's argument(s). See this thread:

Variable Meaning

$_ or !$ Last argument (also Alt + .)

!:1, !:2 First, second argument, etc.

!:3-4 Third and fourth arguments

!:0 Previous command

!* All arguments to last command
Find Recently Modified Files

Find files modified less than 15 minutes ago:
```
find / -mmin -15
```
Find and Delete Files Older than x Days

You can see files older than 20 days with:
```
find results/bgc/2000loci/* -mtime +20
```
If you want to do something to those files, add -exec, the command, and then {} \;. For instance, this applies ls -lh to files older than 20 days:
```
find results/bgc/2000loci/* -mtime +20 -exec ls -lh {} \;
```
And this deletes them:
```
find results/bgc/2000loci/* -mtime +20 -exec rm {} \;
```
Duplicate STDOUT to STDERR
```
echo “Whatev” | tee /dev/stderr
```
Add Newline to End of File

Adds \n at the end of the file if needed. Works on OSX.
```
sed -i '' -e '$a\' faulty_file.txt
```

Variable	Meaning
`$_` or `!$`	Last argument (also `Alt + .`)
`!:1`, `!:2`	First, second argument, etc.
`!:3-4`	Third and fourth arguments
`!:0`	Previous command
`!*`	All arguments to last command

Curly Bracket Expansion

Anything in braces expands:

cp important_file.txt{,_backup}
rm really/long/path/{alpha,beta}
touch {a..k}.txt
rm section-{1..9}.txt

Circumflex Command Editing

Not sure what the name of this is, but useful for typos and changing parameters in long commands. Note that only first instance is changed.
```
head ~/Desktop/tmp_line_counts.txt
# ...
^Desktop^Documents
# Runs "head ~/Documents/tmp_line_counts.txt "
```

CSS

Setting margins

Order is Top, Right, Bottom, Left. TRBL! Mnemonic: TReBLe clef.
```
margin: 0px 25px 50px 75px;
```

HPC

Loading Modules, Seeing Effects

module avail gives you the available modules.

module load [module name] loads the module.

module display [module name] tells you what the module will do to you environment.

$ module display abyss/intel/1.3.2
---------------------------------------------------------------
/share/apps/modules/modulefiles/abyss/intel/1.3.2:

module-whatis ABySS: Assembly By Short Sequences - a de novo... 
conflict      abyss 
module        load intel/11.1.046 
module        load openmpi/intel/1.4.3 
prepend-path  PATH /share/apps/abyss/1.3.2/intel/bin 
prepend-path  MANPATH /share/apps/abyss/1.3.2/intel/share/man 
setenv        ABYSS_ROOT /share/apps/abyss/1.3.2/intel 
---------------------------------------------------------------

Submitting Array Jobs

You can submit array jobs with qsub using the -t flag and a range of numbers or commas:
```
$ qsub -t 0-100 myjob.pbs
```
The job array index is stored in PBS_ARRAYID. NYU has a handy wrapper that lets you submit jobs in a range of numbers with a step size:
```
$ qsub -t 0-10:3 myjob.pbs
```
which would run with 0, 3, 6, and 9 as PBS_ARRAYID. A handy trick for using array jobs to pull input file names out of a text file is:
```
INPUT_FILE=`awk "NR==$PBS_ARRAYID" file_list.txt`
```
All of this info was stolen from the NYU HPC Wiki.
PBS Environmental Variables

Good reference can be found here. For instance, $PBS_NODEFILE is the path to a file containing a list of available nodes:
```
echo `wc -l ${PBS_NODEFILE} | cut -f1 -d" "`
```

git

Save Progress without Commit

git stash (see here) creates a stack of unfinished changes so you can reapply them later when you're ready to keep working on the half-completed step.
Undo the Last Commit

Undo the last commit and move all changes back to stage. (Must be done before push.)
```
git reset --soft HEAD^
```
Undo the Last Commit and REMOVE Changes

Undo the last commit and REMOVE all changes. (Must be done before push.)
```
git reset --hard HEAD^
```
Undo Multiple Commits and REMOVE Changes

Undo the last two commits and REMOVE all changes. (Must be done before push.)
```
git reset --hard HEAD^^
```
Amend Last Commit

Amend the last commit. (Must be done before push.) Optional commit message will overwrite the original commit message.
```
git add whatev.txt
git commit --amend -m "Add foo.txt and modify whatev.txt"
```
Reset Unstaged Changes
```
git checkout file_to_revert.txt
```

Intelligently Show LaTeX Changes

git --no-pager diff --color-words manuscript.tex

bergeycm/stuff-i-forget

Stuff I Routinely Forget How to Do

Quick Links

Perl

R

Unix/bash

CSS

HPC

git