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viewing_alignment_files [2021/05/12 13:21] – created 168.91.18.151viewing_alignment_files [2023/07/25 12:00] (current) – 134.190.232.186
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 +By Joran Martijn
 +
 If you are working through a remote server or computer cluster like Perun or Graham, and you are generating alignment files, you may want to check quickly the quality of your alignment. Is there anything strange, are the sites properly aligned, is there perhaps one sequence that is clearly not aligned? If you are working through a remote server or computer cluster like Perun or Graham, and you are generating alignment files, you may want to check quickly the quality of your alignment. Is there anything strange, are the sites properly aligned, is there perhaps one sequence that is clearly not aligned?
  
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 However, this requires a lot of actions and key strokes: However, this requires a lot of actions and key strokes:
-1. Open a new terminal window +  - Open a new terminal window 
-2. Look up the location of the alignment file on the remote file system +  - Look up the location of the alignment file on the remote file system 
-3. Decide where you want to have the file on your own file system +  - Decide where you want to have the file on your own file system 
-4. Invoke the above command +  - Invoke the above command 
-5. Type in your password +  - Type in your password 
-6. Open the alignment file with SeaView or AliView +  - Open the alignment file with SeaView or AliView 
-7. Optionally delete the file now that you have seen it+  - Optionally delete the file now that you have seen it
  
 As you might imagine, this is not ideal. As you might imagine, this is not ideal.
  
 Thankfully, there is a tool available that allows you to view alignment files directly in your terminal, even if they are on a remote system! [[https://github.com/mpdunne/alan|Alan]] Thankfully, there is a tool available that allows you to view alignment files directly in your terminal, even if they are on a remote system! [[https://github.com/mpdunne/alan|Alan]]
 +
 +See if Alan is installed on Perun already. If not, install it on your home:
 +
 +<code>
 +$ cd
 +$ mkdir tools
 +$ cd tools
 +$ git clone https://github.com/mpdunne/alan
 +</code>
 +
 +And add it to your $PATH by adding this to your ''.bashrc''
 +
 +<code>
 +# alan - a command line alignment viewer
 
 +export PATH=“~/tools/alan:$PATH

 +</code>
 +
 +You can now view your alignment file simply with
 +<code>
 +$ alan <alignment_file>
 +</code>
 +
 +By default, the coloring of the nucleotides or amino acids can be very bright.
 +If you wish to use less bright colors, find the ''default_p'' line in the alan script ( ''~/tools/alan/alan'' ) and comment it out. Now add the following line
 +
 +<code>
 +# the new value of default_p with TEMPERED COLORS
 
 +default_p="KkRr\t01;31\nSsTtQqNn\t01;32\nAaIiLlMmFfWwVvCc\t01;34\nCc\t0 1;37\nEeDd\t01;35\nGg\t01;33\nHhYy\t01;36\nPp\t01;33"
 +</code>
viewing_alignment_files.1620836518.txt.gz · Last modified: by 168.91.18.151