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rrwick / Porechop

adapter trimmer for Oxford Nanopore reads
GNU General Public License v3.0
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Adds -f flag to use a custom CSV [f]ile of barcodes. #47

Open sclamons opened 6 years ago

sclamons commented 6 years ago

Adds the ability to use custom barcodes defined in a (user-specified) CSV file using a -f flag.

If the flag is on, the first thing porechop.py does is to parse the CSV file into a list of Adapter objects, then append that list to the end of the list of Adapters from adapter.py.

kyrubas commented 6 years ago

@rrwick, first off- great repository. Second, any thoughts on merging this into the main repo? As I would rather not alter the hard-coded adapters file, I'm going to clone this fork for now as it solves my use case. @sclamons, what are your thoughts on adding a second argument to completely over-ride the default adapters rather than append them to the list? Or even having the defaults as a default csv that gets generated into a list of adapter objects rather than a *.py file.