This bioinformatics lesson is brought to you by the letter 'T'

Today's bioinformatics lesson is brought to you by the letter 'T'

by

Keith Bradnam

Today's bloinformaties lessonis brought to you by the letter T1

Tis for Text editorsis for Text editors

There are many Unix text editors!There are many Unix text editors!

Editors Super powers Learning curve

Nano None Shallow

Emacs All of them Very steep

Vi All of them Very steep

Vim All of them Very steep

Editors Super powers Learning curve

Nano

Emacs

Ali

Vim

None Shallow

All of them V e r y steep

All of them V e r y steep

All of them V e r y steep

These editors are available on every Unix system from the terminal

These editors are available onevery Unix system from the terminal

https://en.wikipedia.org/wiki/Comparison_of_text_editorshttps://en.wikipediaorgiwiki/Comparison of text editors

Text editor support for various operating systems416 Windows t 1 OS X * Lin u BSD * Unix 0penV MS *

Acme Yes Yes Yes Yes Yes NoAkelPad Yes N o N o N o N o N oMphatk Yes Yes Yes Yes Yes YesAqua macs No Yes No N o No No

Yes Yes Partiailli • No N oAtomArachnophilla Yes Y e s Yes Yes Yes N oBBEdit No Y e s N o N o N o N oBluefish Yes1 Yes Yes Yes Yes YesBrackets Yes Yes Yes N o No NoCoda No Y e s No N o N o N oConTEXT Yes No No N o N o N oCrimson Editor Yes No N o N o N o N oDiakonos Yes Y e s Y e s Yes Yes Noed Yes Y e s Y e s Yes Yes YesEditPlus Yes N o No N o N o N oEditra Yes Y e s YesEm Editor Yes N o N o N o N o Noepsilon Yes Y e s Y e s Y e s N o

Yes!Yes Yes Y e s Y e sGeany Yes Yesgedit Yes Ye s [ 3 ] Y e s Y e s Y e s N oGNU Emacs Yes Y e s Y e s Y e s Y e s Y e sGobby Yes Y e s Y e s Y e s Yes NoJED Yes Yes Y e s Y e s Yes Yes'Edit Yes Yes Y e s Y e s Yes NoJOE Partialm Yes Yes Y e s Yes NoJOVE Yes Y e s Yes Yes Yes NoKate Partial[5] Yes Yes Yes Yes NoKEDIT Yes No Yes Yes No NoKod No Yes No No No No

•

Programming features [edit]

, hi

AcmeAkelPadAlphatkAquamacsBBEditBluefishBracketsCodaCon TEXTCrimson Editor

YesYesYesYes

Diakonos

Yes

E Text Editor

Yes

ed

Yes

EditPlusEditraEmEditor

No

Geany

NoYesYesYesYesYesYesYesYesYesYesYesYes

gedit

Yes

GNU EmacsGobby

Yes

JEDjEdltJOE

Yes

JOVEKateKEDIT 1M

Bracematching

Autoindentation

YesYesYesYesYesYesYesYes

YesPlug-inYesYesYesYesYesYes

YesYesYesYes

YesYesYesYesNo • No

YesYesYesYesYesYesYesYesYesYesYesYes

•YesYesYesYesYesYesYesYesYesYesYesYesYes Yeses

Syntaxghlighting

NoPlug-inYesYesYesYesYesYesYesYesYesYesNoYesYesYesYesYesYesYesYesYesYesNoYesYes

Functionlist

YesPlug-in

YesYesNoYesYes

No

No

NoYes

Plug-in

Plug-in

Text editor support for programming features (see source code editor)Symboldatabase

(ctags or equiv.)Yes

Yes

NoYes

Partial(45)Partial

M r N7—.1Pat a05)

Plug-inYes[49)Plug-inYesNoYes

Yes

Plug-inMacro

YesYes

YesYesYesYesYesYes

YesYes

Autocompletion

YesPlug-in

Yes

E N o I

• N oYes[471

Plug-in 1481Yes

Plug-inYesNoYesYes

• N o IYes

• N o

Codefolding

• N oPoug- nYesYesYesYesYesYesNoNo

• N oYes

• N oYesYesYes

PartialNoYes

• N oYesYesNoNoYesYes

Textfolding

NoNoYesYesYesNoYesNo

No INoNoYesNoNo

YesNo

Plug-in(50YesNoYesYesNoNoYesYes

CompilerIntegration

YesPlug-inYesYesYes

Yes1441Plug-in

NoYesYesNoYesNoYes

YesYes

Yes[51IYes• NoYes

Plug-inYesYes

Plug-inYes

Tis for Timeis for Time

It takes time to learn command-line skillsIt takes time to learn command line skills

But those skills will always remain useful!But those skills will always remain useful!

Future usefulness of various skillsWindows 10

skillsBioinformatics

programsUnix

commands

Today � � �1 year from now � � �

5 years from now ? � �10 years from now X ? �20 years from now X X �

Future usefulness of various skillsWindows 10

skillsBloinformatics U n i x

programs commands

Today

1 year from now

5 years from now

10 years from now

20 years from now

t t t

X ? i f

Keep learning!Keep learning!

Tis for Tab-completionis for Tab-completion

esc

0,0 11„

2

option

w 1

I:230 17:7

3

F

•••••command

ODDODD F4

4 5A6 &7

44

8

)11

19

•••::ommand option

ril

1

4))) F12

A

delete

Tab-completion is your friendTab-completion is your friend

Tab-completion will probably save you more time than anything else you will learn

Tab-completion will probably save you moretime than anything else you will learn

The endThe end