I want to check if there are gene clusters (consecutive genes with the same function) on each chromosome. So I have the gene genomic orders (coordinates), and function (pfam/gene family etc) for each gene.
Such as adding prefix, replacing strings, removing suffix etc.
I encountered several times when trying to cp/rm/cat >10000 files on Mac. Just a note for the solutions.
This is originally from the work that I was trying to find enriched functional clusters on chromosomes. I made 5-gene sliding 50-gene blocks and tested functional enrichment in each block.
Set a bash variable from a command and process with argument.
Using bash associative array to make pairwise alignment of sequences