Difference between revisions of "I2rda Course Cheatsheet"

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* <code>ctrl + d</code>: delete a character (useful when used after above)
 
* <code>ctrl + d</code>: delete a character (useful when used after above)
 
* <code>ctrl + e</code>: go to end of line
 
* <code>ctrl + e</code>: go to end of line
 +
* <code>alt + b</code>: move backwards word-wise.
 +
* <code>alt + f</code>: move backwards word-wise
 +
* <code>alt + d</code>: delete current word forwards, next word if in space
 +
* <code>ctrl + k</code>: delete to end of line
 
* <code>ctrl + w</code>: delete current word backwards, word behind if in space
 
* <code>ctrl + w</code>: delete current word backwards, word behind if in space
 
* <code>ctrl + y</code>: yank, or paste most recent deletion (useful when used after above to repeat deletion)
 
* <code>ctrl + y</code>: yank, or paste most recent deletion (useful when used after above to repeat deletion)
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* <code>ctrl + x, <BACKSPACE></code>: search backwards for a character, here?
 
* <code>ctrl + x, <BACKSPACE></code>: search backwards for a character, here?
 
* <code>ctrl + r, ?</code>: search backwards for a character, here?
 
* <code>ctrl + r, ?</code>: search backwards for a character, here?
* <code>alt + b</code>: move backwards word-wise.
 
* <code>alt + f</code>: move backwards word-wise
 
* <code>alt + d</code>: delete current word forwards, next word if in space
 
* <code>ctrl + k</code>: delete to end of line
 
  
= Pagers: <code>man</code>, <code>less</code> and <code>vim</code> keys =
+
= Pagers: <code>man</code>, <code>less</code>, <code>vim</code> and <code>R</code>-help =
  
 
* <code>q</code>, to get out again.
 
* <code>q</code>, to get out again.

Revision as of 12:23, 11 May 2017

Ways of getting out of things

  • Typing exit (the terminal, command-line, queue system, screen program)
  • Ctrl+C, usually interrupts a process
  • q()in R.
  • q in less and xpdf
  • alt-F4, sometimes for R plots for instance.
  • Ctrl+W, to close a tab.

the module software loading program

  • moduleav to see what's available
  • moduleav |grep samtools to see only those lines containing samtools
  • module help samtools, to see any possible help information (samtools in this case) on the module (not always informative).
  • module list to see your currently loaded software modules
  • module load samtools to load a certain (samtools in this case) module (Default modules do not need version numbers).
  • module unload samtools to unload a certain (samtools in this case) module (Default modules do not need version numbers).

GNU screen program

  • type screen to get in.
  • type exit to get out of your screen sessions
  • ctrl+l, n: cycle through screen windows
  • ctrl+l, :hardcopy RET: create a file with a copy of all inputs and outputs of your session.
  • ctrl+l,d: detach screen session
  • type screen -r to recover a detached session.
  • ctrl+l,K: abandon current session. It will be lost.
  • ctrl+l,ESC: enter scroll or copy mode. PgUp an PgDn will now work. Esc to get out.

Graphical programs

  • Note Using graphical programs on the cluster is slow, because very many pixels all have to be sent down the network.
  • to view pdf files: xpdf <file.pdf>.q will exit.
  • to view spreadsheet, tsv or csv files: gnumeric <file.csv>. Alt-F4 to get out.
  • When R pops up a plot, Alt-F4 to get out.

Command-line Navigation

(majority of these work both on Unix/Linux command-line and in the R interpreter)

  • ctrl + a: go to beginning of line
  • ctrl + d: delete a character (useful when used after above)
  • ctrl + e: go to end of line
  • alt + b: move backwards word-wise.
  • alt + f: move backwards word-wise
  • alt + d: delete current word forwards, next word if in space
  • ctrl + k: delete to end of line
  • ctrl + w: delete current word backwards, word behind if in space
  • ctrl + y: yank, or paste most recent deletion (useful when used after above to repeat deletion)
  • ctrl + /: undo changes
  • ctrl + x, <BACKSPACE>: search backwards for a character, here?
  • ctrl + r, ?: search backwards for a character, here?

Pagers: man, less, vim and R-help

  • q, to get out again.
  • gg, for top of the page
  • G, for bottom of page
  • Ctrl+f, to advance one page forward.
  • Ctrl+b, to move one page back.
  • / to search, it allows you type in a search term at the bottom.
  • The up,down,PgUp and PgDn keys all work as expected.

Linux shortcut symbols

  • . the directory you are currently in, often used with mv, cp or ln -s to mean "in here please"
  • .. the directory one level above the one you are currently in, aka. the parent directory
- To change directory to the one above your are in: cd ..
  • To returns to the last directory you were working in before this one: cd –
  • On its own, cd bring you to your home directory
  • ~ shorthand for your home directory, where all your data is kept.
  • > directs output of one command into a file
  • | often called the pipe operator: directs output of one command into another command.

Keybindings for using the history file

  • :<RET>: save command in history, do not execute.
  • !$<RET>: the final argument of the last command
  • !!<RET>: the entire last command
  • !:1-$<RET>: everthing except the first word of the last command
  • !$<RET>: the final argument of the last command
  • ^then^now<RET>: replace the first occurence of then in last command with now
  • !!:gs/then/now/<RET>: replace the ALL occurences of "then" in last command with "now"
  • !!:gs/then/now/:p<RET>: as above except do not execute.

Using vim

  • type vim to get in, and :q! to get out without saving.
  • ZZ to save onto to current filename. ":sav fname" otherwise
  • It opens in "normal" mode which is similar to less, in that direct editing is not expected.
  • This is changed by pressing i. To get back to normal mode, press the ESC key.
  • In normal mode u undoes any changes
  • : while in normal mode allows command sto be entered
  • Visual: enabled by "v" or "V" (visual block), sub-box at the bottom open.
  • After v or V, movement keys ":%" will operate on whole document, ":’a,’b" operate between two marks, ":42,45" between two line numbers
  • search via "/", ":set hlsearch" to see all the hits

Getting by in only normal mode

  • movement keys, "w" jump via start of words; "e" jump via ends; "fc" jump to next c
  • "0" for start of line, "A" for end of line and into insert mode
  • "x" delete current character, "xp" switch positions of current and next character
  • "yyp" copy current line and paste it underneath
  • "dd" delete line, "2d" delete this and following two lines. "dgg" delete to start, "dG" delete to end
  • "dw" delete current word
  • Command: Activated by ":", sub-box at the bottom open, rich command language
  • Visual: Activated by v or ctrl+v (visual block), sub-box at the bottom open, rich command language

Advanced but really useful commands

  • :colorscheme desert change to the desert colour scheme, there are many others: morning, delek.
  • :%s/snooze/sneeze/gc also works
  • :g/sneeze/d delete all lines without sneeze"
  • :v/sneeze/d delete all lines with sneeze"
  • ":42y[RET]p" paste line 42
  • "d214G" delete up to line 214
  • "y214G" copy up to line 214
  • :set list, all non-printing characters are also shown.
  • :set hlsearch, will highlight all search occurrences.
  • :set nu, show line numbers.

a fast pdf viewer: xpdf

  • xpdf mypdffile.pdf opens mypdffile.pdf using the X11 graphical system
  • q to get out
  • + to maker bigger
  • - to make smaller
  • Spacebar for bottom of page
  • n for next page
  • p for previous page
  • alt+f toggle for full screen and back

IGV Genome browser keys

  • ctrl-R Defines the region currently in view as a region of interest.
  • ctrl-F/ctrl-B Skip forward to the next feature and back to the last feature.
  • ctrl-shift-F/ctrl-shift-B If you have the feature track expanded and have selected one of the rows, this will skip forward to the next exon or back to the last exon.
  • alt-left/alt-right, move you back and forward through your IGV history.
  • Arrow-keys Pans left, right, up, and down in the current chromosome.
  • Home/End-keys Skips to the page top or bottom of the current view, then pages right or left respectively.
  • PageUp/PageDown-keys Pages up and down the current view.