Awk

I wanted a simple way to see the progress of a data processing pipeline, and the internal progress bar tools were messed up by threading. I thus decided to use the number of output files in each folder as an indicator of progress. In my case the output of tree . looks like this: . └── steps ├── A01_001 │ ├── segment_nuclei │ │ ├── 0000.npz │ │ ├── 0001.npz │ │ ├── ... │ │ └── 0019.npz │ ├── tile │ │ ├── 0000.npz │ │ ├── 0001.npz │ │ ├── ... I can get the info I need by counting the total number of files and the occurrences of the A01_001 -> P24_005 range (these are fields of view from a microscopy experiment). Using this simple find command we get all the files in the current folder. ...

I was editing some markdown and had to insert a new figure in the middle. The problem is that this document already has an explicit figure numbering (e.g., “Figure 5”), so changing tens of figures felt dull. I like to run small (GNU) awk scripts for this type of tasks. # update_figures.awk { if (match($0, "Figure ([0-9]+)", num)){ if (num[1] > after){ gsub("Figure ([0-9]+)", "Figure " num[1] + increase_by) } }; print $0 } This changes Figure X into Figure X + increase_by starting after the variable “after”. And we can run it as follows: ...