prefix2id.py replaces Illumina prefixes (e.g., 1_S01_L001...) with sample ids (my_sample1_S01_L001...) in multiple files.
To do this, you need to specify a file with a table of numbers and names, and a directory containing files to be renamed. Additionally, you can specify the Illumina lane number.
There are 2 columns (number and sample_id) in the table separated by tab:
1 my_sample1
2 my_sample2 ...
Also, it transforms spaces and brackets in sample_ids to underscore.