Convert sampled sequences back to alignment file

[benjamin-lieser]

I have read the tutorial and have successfully computed the sample matrix from the sample method. Now I want this sequences in a fasta file (or similar). Is there an easy way to do this here, or at least some documentation on the coding from amino acids to the numbers in this matrix?

[pagnani]

Hi @Unlikus

Indeed we did not provide this utility. However, you can define this function

function my_write_fasta(filedest::String, Z)
           num2let = ['A', 'C', 'D', 'E', 'F', 'G', 'H', 'I','K', 'L','M', 'N','P','Q', 'R', 'S','T', 'V', 'W', 'Y','-']
           N,M = size(Z)
           open(filedest,"w") do fp
               for s in 1:M
                   println(fp,"> Seq $s")
                   for a in 1:N
                       print(fp,num2let[Int(Z[a,s])])
                   end
               println(fp)
             end
           end
end

where:

• filedest is the name of the file where you want to write the results
• Z is a matrix containing the generated alignment (a matrix of size N x M where N is the MSA length and M is the number of samples generated).

So, as an example, you could run the following pipeline:

julia> arnet,arvar=ardca("data/PF14/PF00014_mgap6.fasta.gz");
julia> Zgen=sample(arnet,10000)
julia> my/write_fasta("foo.fasta", Zgen)

Last thing, if you want to define the function it is enough to copy and paste the definition above, either on the REPL or in a jupyter cell.

Let me know if you have any other problem

[benjamin-lieser]

Thanks a lot :)