First, many of you will have to forgive my minimal programming skills but I am trying to write a program that will take 2 paired very large multiple-sequence FASTA file (each have >77,000 sequences) and get an alignment score of the sequences. My current implementation of the problem has had the problem that it uses to much memory. To get around this I split the multiple-sequence fasta files into a bunch of smaller files to feed in one-by-one. Still after getting around the 38th score I get a MemoryError: Out of memory exception. I will attach my code but I was wondering if anyone had any suggestions of fixing this issue or simply getting the alignment scores for the list. Please help I hope I am being clear and again forgive and verbose/ bad code,
I tried to copy and paste my code but it ended up being really messy so I have simply attached a link.
Anyways any help is greatly appreciated and I hope you are all having a great Tuesday and PLEASE PLEASE PLEASE HELP IF YOU ARE ABLE TO!!