Some enhancements!

[palmhjell]

First off just reiterating this is so amazing. I love it.

Okay down to business, in order of decreasing priority/increasing complexity:

1. In the README, be more specific about how the reverse RefSeq is literally just as easy as it sounds (the 5' to 3' direction of the gene itself). I can make this change, just putting it here for reference.

2. Output a third file in Summary, which is just the stats for the max in each well. (Easy code, can do it after, but also would be nice to just have.) Then if >95%, feel confident. If lower, check on a case-by-case basis if acceptable or meaningful.

3. Add more automation in the sequence generation for the RefSeq.csv file. For example, if doing a single plate, allow passing 'all' in the well position, which would specify applying the ref sequences for all wells in a plate (A–H, 1–12). Or pass a list of plates if doing more than one.

4. Let the parser read zipped files. (This may be as simple as just changing the function used for reading... https://stackoverflow.com/questions/12902540/read-from-a-gzip-file-in-python. It also might not...)

[kadinaj]

1. Building off the RefSeq comment, you can make it clearer where you should start with the sequence. Ex. from the beginning of the primer, from the end of the primer, etc.

2. Building off of Patrick's Parameters #3, I agree. Maybe you could have a small script here that autogenerates this csv for you since really the only information I needed to provide (at least for a single plate) was the (1) name, (2) number of variable positions, (3) forward sequence, (4) reverse sequence.

[palmhjell]

Agreed @kadinaj. I'm going to make a branch and quickly address #1, #2, and #4 since those are very easy. #3 should be its own thing since it's a bit more involved.

[kadinaj]

3. Pass the file location of the GlobalParams.txt file when calling the program so that you can avoid needing to have it in the same folder as the script

[palmhjell]

We should also make the Summary outputs include the actual codons at each position, since L and I (?) have two possible codons and that can very possibly make a difference in activity. (Or, if we don't use the 22c trick, it would be more critical.)

[palmhjell]

Moved the 3rd issue here to a new stand-alone issue (#3).

[palmhjell]

Closing for next round of updates.