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https://github.com/mpdunne/alan

Alignment viewer for linux terminal
https://github.com/mpdunne/alan

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Alignment viewer for linux terminal

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README 

        
![alt text](http://empede.co.uk/imgrepos/Alan_head.png? "Alan header")



# Alan — a simple in-terminal alignment viewer



Alan is a simple, light command line alignment viewer, for viewing amino acid and DNA alignments in a linux terminal.



It can be used for viewing FASTA or Clustal format alignment files, and relies on just a few standard unix packages.



Current Alan version (2.1.0): https://github.com/mpdunne/Alan



Usage

=====



Alan is essentially a modified version of the ubiquitous ```less``` text reader. It uses a number of very common unix tools (```awk```, ```sed```, ```grep``` among others).



The ```alan``` command should be ready to use straight out of the box - no installation is required. Just type:



```/path/to/alan your_alignment.fa```



Where ```/path/to/alan``` is wherever you've saved the `alan` file in this repo.



To make things even easier, you may wish to add the directory containing the ```alan``` executable to your ```$PATH``` by editing the ```.bashrc``` (or ```.zhrc``` if you're on a mac) file in your home directory (e.g. add the line ```PATH=$PATH:/path/to/alan_dir```). Alternatively you can specify a shortcut in your ```.bashrc``` or ```.bash_aliases``` file by adding the line ```alias alan="/path/to/alan"```. If you've done either of these, Alan can be run by simply typing ```alan your_alignment.fa```.



Alan sometimes struggles with larger alignments.



File types and options

======================



Alan works on FASTA and Clustal format alignments. It's a very basic alignment reader, and any other alignment formats will confuse it. If this is an issue, convert files before viewing. The choice of file format (FASTA or Clustal) is detected automatically. Alan has been principally tested with FASTA files -- raise a support request if you have any trouble with Clustal files.



If no information on molecule type is supplied, Alan will try to detect whether an alignment is composed of protein or nucleotide sequences, and will display them accordingly. To override this, use the options ```-n``` for nucleotides, or ```-p``` for protein sequences.



To navigate the alignment, use the keyboard arrow keys. The amount by which an alignment is shifted using the arrow keys can be set using the ```-s``` or ```--shift``` options, followed by a numeric value. The default is 10.



Alan uses ```less``` as its main viewer, and so any other in-viewer commands contained in less will also work in Alan. This includes searching (use ```/```), and more: see https://en.wikipedia.org/wiki/Less_(Unix) for a few.



Colours

=======

By default, Alan uses the clustal colour scheme as described [here](http://www.jalview.org/help/html/colourSchemes/clustal.html). The formatting is not context-dependent, and so always displays one colour per character. The formatting is designed to work on a black-screen terminal.



You can update the colour scheme used by Alan in two ways. Alan colour schemes are defined by colour files. The default one for protein alignments looks like this:



```

-                  0;0

KkRr               01;41

SsTtQqNn           01;37;42

AaIiLlMmFfWwVvCc   01;44

Cc                 01;105

EeDd               01;45

Gg                 01;90;103

HhYy               01;46

Pp                 01;90;43

```



The default one for nucleotide alignments looks like this:



```

-Nn     0;0

Aa      01;31

Gg      01;33

Cc      01;32

Tt      01;34

```



These are tab-delimited text files, and are embedded in the alan script itself. The first column defines the symbols to be coloured, the second defines the formatting and colouring using the codes from [here](http://misc.flogisoft.com/bash/tip_colors_and_formatting). Different formatting instructions are separated by ```;```, so that for example ```01;90;103``` means ```01``` (bold) and ```90``` (dark grey text) and ```103``` (light yellow background). Finally, the colour file must not contain blank lines, and any instance of "```-```" must be at the start of a line.



To include a custom colour file, include a ```colp.csv``` or ```coln.csv``` file (for protein and nucleotides respectively) in the same directory as the ```alan``` file, the contents of which should be in the same format as the above. Alternatively, if you wish to use multiple colour schemes for different purposes, you may wish to explicitly refer to a colour scheme file using the ```--colp``` or ```--coln``` options. For example:



```alan my_alignment.fa --colp my_colours.csv```. 



Examples

=====



![Alt Text](http://empede.co.uk/imgrepos/aa.png "Alan Davies")

![Alt Text](http://empede.co.uk/imgrepos/cds.png "Alan Rickman")



The Alan museum

===============



The original Alan command was a one-line modification of the ```less ``` command. For its simplicity and portability, you may wish to use the orignal alan on your system. This and some derived commands are contained in the alan_museum directory, and they are loaded as functions, so type ```source alan_museum/alan_orig.sh``` to load them, and then type the individual commands to use them. The original Alan commands are:



| Command Name   | Command         | Description           | Example                               |

|----------------|-----------------|-----------------------| --------------------------------------|

| Alan Bennett   | `alanbennett`   | Fasta, automatic      | ```alanbennett alignment.fasta```     |

| Alan Davies    | `alandavies`    | Fasta, protein        | ```alandavies prot_alignment.fasta``` |

| Alan Rickman   | `alanrickman`   | Fasta, nucleotide     | ```alanrickman nuc_alignment.fasta``` |

| Alan Partridge | `alanpartridge` | Clustal, automatic    | ```alanpartridge alignment.fasta```   |

| Alan Menken    | `alanmenken`    | Clustal, protein      | ```alanmenken prot_alignment.fasta``` |

| Alan Shearer   | `alanshearer`   | Clustal, nucleotide   | ```alanshearer nuc_alignment.fasta``` |