Great outline! I honestly cannot find anything to critique on. Your algorithm is very well written, and I can easily follow it. It does everything the assignment asks for. I think it’s a fantastic idea that you only store a single record at a time since these are huge files.

Your revcomp function also seems well planned out. Nicely done!

Christina,

Really well written pseudo code! Just some thought I had when I was reading it!

“For each pair of indices we will determine which bucket it should be sent to and output the 4 lines for each pair of reads to either the R1 or R2 file in corresponding bucket”

You explain this in detail further down but maybe throw on a “general idea for this code” label? I was a touch confused about how and what was going to take place.

“For the 2 read FASTQ files and 2 index FASTQ files, will extract one read at at time (line by line) and append the read to its appropriate bucket file”

You’re appending the full, 4-line record here, yeah? Not just the sequence line?

“If index1 and index2 RC are in the index dictionary // could be either matched or swapped
If index1 and index2 both meet the quality score cutoff:”

I wonder if these couple lines in this order might illicit some errors for you?

Instead of running to check if these potential error indicies match the index dictionary (we know they probably wont make the cut) why can’t we just trash everything if they don’t make the cutoff first?

“Else if either or both indexes don't meet cutoff:”

The quality score cutoff or if we don’t know what the indicies are?

Might be good to know exactly what data we are getting ‘rid’ of and what exactly that means? Are we sure we want to trash all the unknown reads?

“output the modified header to each file”

Same header for both read files? How might you be telling them apart as Read 1/Read 2 when all is said and done?

Functions are looking good might want to throw in some “N’s” in there on the rev comp function just as a contingency in case your code pics up an ‘N.’ That way you could use it later too if you want :)

For your pseudocode:

1. Very detailed and organized
2. Good use of using a dictionary to store your indexes and if statements to organize your reads.

Optional:

1. Move your quality score cut off to your first conditional statement, b/c if that isn’t met, there's no use of going through your other conditional statements.
2. Replace counter with enumerate

For your Function:

1. Steps are clearly written out and examples are good

Nice work ☉ ‿ ⚆