Hello everyone, I am super new to perl and after I was slowly starting to get the hang of it, I got sick. And since then I have been on a health break for around four months. You can imagine that I am now once again completely lost when it comes to scripting. I need to pick up my work again now, but I am honestly lost and a bit overwhelmed...if not even scared about how and where I should even start. I tried reading through some tutorials, but sadly those only worsened my anxiety with scripting.

All I am able to provide is a pseudo-code...or some sort of it, that I wrote down in order to see what my new script needs to do. However my first struggle is already fitting the regular expression in the first step. I do NOT expect anyone to write me down a script now, as I would love to be able to work on it myself. But I believe I do require some pushes into the right direction, some advice on how to tackle this script. Thank you very much in advance.

1. Create a header with all the IDs
- open/create file
- start header file with "Source tRNA"
- get ID via regex UNI_DATE_ID_ENDING_#NO
- add ID to file
- close file

2. Create new files
-Titles:
5p-tR-halves
5p-tRFs
p-tR-halves
3p-CCA-tRFs
3p-tRFs
tRF-1
tRNA-leader
misc-tRFs

- add first column to each file:
MT-TA
MT-TC
MT-TD
MT-TE
...

3.
- print the according columns from each mergerpt file from each folder
+ into the new file
- column assignment:
5p-tR-halves - 1
5p-tRFs - 2
p-tR-halves - 3
3p-CCA-tRFs - 4
3p-tRFs - 5
tRF-1 - 6
tRNA-leader - 7 
misc-tRFs - 8

4. Add the ID header to each file

[download]

I have multiple folders and they all contain a file with the same name ("merge") which I am working with. The file roughly looks like that:

MT-TA    5.36272153463324    21.4508861385329    8.04408230194985    3
+4.857689975116    0    0    0    13.4068038365831
MT-TC    24.1322469058496    160.881646038997    48.2644938116991    3
+7.5390507424327    45.5831330443825    0    0    104.573069925348
MT-TD    10.7254430692665    10.7254430692665    0    2.68136076731662
+    0    176.969810642897    1.34068038365831    445.105887374559

[download]

The goal is to have new files which all have the 1st/2nd...column from these merge files. So the first new file should contain just the 2nd column (because the first is the source name) from all "merge" files; the next just the 3rd column from all files, the next just the 4th...and so on.

Any help and advice on how I can start working on, or where I can turn to, to find what I need to write this script is much appreciated. ~Panda

In reply to General Help/Advice Needed by PandaRaey

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