gene | Grace , fastest , flexibility , simple PHP extension

I have the following data frame:

I have the following data frame:

I have a data set similar to this tibble:

I need to submit a slurm array that will run the same script 18000 times (for independent genes), and I wanted to do this in a way that won't cause problems for my Uni's cluster.

Currently, the MaxArraySize set by the admins is 2048. I was going to manually set my options like:

First array script:

I have the following dataframe:

I am struggling to separate a single string input into a series of inputs. The user gives a list of FASTA formatted sequences (see example below). I'm able to separate the inputs into their own

ex:

my dataframe looks like this:

I'm trying to use fuzzy string matching to convert strings to specific ids and perform grouped summarization using dplyr. The basic idea is combining imperfect gene sequences into a single gene name via a dictionary lookup approach and counting how many times the gene is detected. This way, counts for sequences aaaaaa and aaaxaa match to gene1 and get added together.

I can do what I want using for and if statements via a row-by-row comparison of the raw data against the dictionary but I find this will be inefficient when I scale up (raw data files have 15k rows on average, the dictionary has 200 rows). Please see my solution below I'm trying to improve and let me know if you can think of a more efficient and elegant way of doing this.

I have a tab delimited binary matrix of bacterial strain names and genes, listed as present (1) or absent (0), which is output by ROARY (pangenome pipeline).

This is a mock version of the data: