Bash$/$Linux

The gene expression data is currently split up into several files within various subdirectories of the $/$rds$/$homes$/$u$/$username$/$xxxx$/$Matrix directory.

Write a Bash script that can be run within the Matrix$/$directory to process the gene expression matrices to produce the following two output files:

A single csv file containing the gene expression matrix for variety X$,$ including the header line. You should name this file GEM$\_$X$.$csv $($GEM stands for Gene Expression Matrix$).$

A single csv file containing the gene expression matrix for variety Y$,$ including the header line. You should name this file GEM$\_$Y$.$csv

In the file headers, each sample name for the columns of the matrix currently has the following format:

Variety, followed by condition code $($C$,1,2$ or $3)$ and biological replicate $($a$,$b or $$c$).$ C is the control, and $1-3$ are the stress conditions. For example, VarXC$-$a denotes Variety X$,$ Treatment C and replicate $$a$.$

Header for VarX: gene$\_$name,VarXC$-$a$,$VarX$1-$a$,$VarX$2-$a$,$VarXC$-$b$,$VarX$3-$b$,$VarX$1-$b$,$VarX$2-$b$,$VarXC$-$c$,$VarX$3-$c$,$VarX$1-$c$,$VarX$2-$c

Your gene expression matrix files should:

Contain only unique genes located on the $12$ chromosomes, with genes sorted by chromosome.

Change the column labels in the header to a more convenient format, replacing $$a with Rep$\mathrm{.}1,-$b with Rep$\mathrm{.}2$ and $$c with Rep$\mathrm{.}3.$ In the above example, VarXC$-$a becomes VarXCRep$\mathrm{.}1$