Added a fastq file parser

[fragilefort]

Added a fastq file parser. Let me know if anything need documentation or fixes. It can work with both files and multiline sequences. Note: motif.py has some issues and importing Dna class in fastq.py will case issues so before testing the parser, comment out lines in the init.py in analysis which imports motif.py until this file is fixed.

[dawnandrew100]

So, it looks like the reason why the tests aren't passing is because of the numpy import. I think that's more of an issue with the action runner itself rather than the implementation, so I'm going to see what the minimum number of changes I need to make are to make that work.

I think I just need to add numpy to the dependencies of the pyproject.toml

The issues in motif.py might be the nested f-string, which isn't supported prior to Python 3.12
If you're using a version before that, it might be causing you trouble
For that, I think I just need to have different quotation marks for the nesting to work, so we'll see

[dawnandrew100]

Okay, so the problem was that GitHub didn't acknowledge that the pyproject.toml said requires-python = ">=3.10" instead of requires-python = ">=3.12", but we did some voodoo, and now that is fixed

Will look at fastq.py properly in the morning
A few things I can see from a quick glance that should be changed

1. Need to add a testing suite to the tests folder for the new fastq functionality
2. Read -> FastqRecord for naming consistency with fasta.py
3. Improve homogeneity between fasta.py and fastq.py (which honestly will most likely be me updating fasta.py where I see fit)
4. Take out the gc content method from Read (no need for it here)

If you want to tackle 1, 2, and 4, that'd be great !

[fragilefort]

Great, whatever it takes to convince him. I will complete 1,2 and 4 today and solve any additional comments with the implementation after review

[fragilefort]

I did the mentioned edits on the fastq parser, and added a test suite and passed with pytest, also tested this time with python 3.13. For some reason, the GitHub test actions complains again about numpy :(

[fragilefort]

So here is the thing, fetching didn't include the changes you did in this pull request so I did the changes pushed and it failed. Then I made the reapply the changes you made earlier today and it only passes 2 builds, not sure where to correct it this time.

[dawnandrew100]

Will have to look over this tomorrow when I'm more awake, but basically, the changes that I made were to make fastq and fasta more uniform in their implementation

Obviously, not everything can be identical because they are two different file formats, and some of the attributes (like phred scores) are unique to fastq files, but the effort was to get close enough so that effectively the same methods could be used on either fasta or fastq

I also converted the fasta parser to a class that has an iterator (but also left the plain function just in case someone might find that useful), and I also added a plain fastq_parser function to fastq.py for the sake of file uniformity

[dawnandrew100]

I'll also leave a comment here to remind myself to make another pull request after this one is merged that will officially bring back support for 3.10 and 3.11 testing through github actions

[dawnandrew100]

This comment is a reminder to myself that I need to remove pytest from the project dependencies and add it to the optional dev dependencies

Something like

[project.optional-dependencies]
dev = ["pytest"]

And anyone working on the project can either just download pytest directly or pip install like this pip install biobase[dev]

[dawnandrew100]

Everything looks good to me!