Feedback script

[rvosa]

• [ ] it would be better if the names of the input files could be provided as command-line arguments with argparse rather than being hardcoded
• [ ] it would be more efficient if you did a targeted search for the genes of interest rather than parsing out all annotations, which you appear to be doing here
• [ ] unless there are things preventing you from doing so (e.g. memory issues) I would recommend you use a gff3 parsers library rather than rolling your own.
• [ ] it is a lot more efficient if you use fastacmd with subprocess (capturing the stdout) to extract the sequence from the FASTA file, rather than iterating through the entire genome within python.

[hfrijmann]

First point is true, we went for functionality first as a argument parses is new territory and not strictly necessary (although desirable) for functionality. It is planned to be included on a later time. The targeted search is done by a simple selection step done by a script that has not been uploaded yet, as it's created by another project member! So when this script reads the GFF3 file it does search for ALL genes, but that GFF3 list will only contain the genes of interest. The other two recommendations are solid! I will review these and update the program when necessary!

[rvosa]

Ok, sounds good. If the splicing is a two-step process (I agree that that is reasonable) then go ahead and do it that way, just make sure you document this clearly. Good luck on the other issues: if you think you have reasonably addressed them you can check their respective boxes so that we can see how we're progressing.