Gget

- **New modules:**
- [`gget cbio`](cbio.md)
- [`gget opentargets`](opentargets.md)
- [`gget bgee`](bgee.md)
- **[`gget enrichr`](./enrichr.md) now also supports species other than human and mouse (fly, yeast, worm, and fish) via [modEnrichR](https://maayanlab.cloud/modEnrichr/)**
- [`gget mutate`](./mutate.md):
`gget mutate` will now merge identical sequences in the final file by default. Mutation creation was vectorized to decrease runtime. Improved flanking sequence check for non-substitution mutations to make sure no wildtype kmer is retained in the mutation-containing sequence. Addition of several new arguments to customize sequence generation and output.
- [`gget cosmic`](./cosmic.md):
Added support for targeted as well as gene screens. The CSV file created for gget mutate now also contains protein mutation info.
- [`gget ref`](./ref.md):
Added out file option.
- [`gget info`](./info.md) and [`gget seq`](./seq.md):
Switched to Ensembl POST API to increase speed (nothing changes in front end).
- Other "behind the scenes" changes:
- Unit tests reorganized to increase speed and decrease code
- Requirements updated to [allow newer mysql-connector versions](https://github.com/pachterlab/gget/pull/159)
- [Support Numpy>= 2.0](https://github.com/pachterlab/gget/issues/157)

- **New module: [`gget mutate`](./mutate.md)**
- [`gget cosmic`](./cosmic.md): You can now download entire COSMIC databases using the argument `download_cosmic` argument
- [`gget ref`](./ref.md): Can now fetch the GRCh37 genome assembly using `species='human_grch37'`
- [`gget search`](./search.md): Adjust access of human data to the structure of Ensembl release 112 (fixes [issue 129](https://github.com/pachterlab/gget/issues/129))

Fix Windows bug in gget elm setup

- **[`gget search`](./search.md) and [`gget ref`](./ref.md) now also support fungi 🍄, protists 🌝, and invertebrate metazoa 🐝 🐜 🐌 🐙 (in addition to vertebrates and plants)**
- **New module: [`gget cosmic`](./cosmic.md)**
- [`gget enrichr`](./enrichr.md): Fix duplicate scatter dots in plot when pathway names are duplicated
- [`gget elm`](./elm.md):
- Changed ortho results column name 'Ortholog_UniProt_ID' to 'Ortholog_UniProt_Acc' to correctly reflect the column contents, which are UniProt Accessions. 'UniProt ID' was changed to 'UniProt Acc' in the documentation for all `gget` modules.
- Changed ortho results column name 'motif_in_query' to 'motif_inside_subject_query_overlap'.
- Added interaction domain information to results (new columns: "InteractionDomainId", "InteractionDomainDescription", "InteractionDomainName").
- The regex string for regular expression matches was encapsulated as follows: "(?=(regex))" (instead of directly passing the regex string "regex") to enable capturing all occurrences of a motif when the motif length is variable and there are repeats in the sequence ([https://regex101.com/r/HUWLlZ/1](https://regex101.com/r/HUWLlZ/1)).
- [`gget setup`](./setup.md): Use the `out` argument to specify a directory the ELM database will be downloaded into. Completes [this feature request](https://github.com/pachterlab/gget/issues/119).
- [`gget diamond`](./diamond.md): The DIAMOND command is now run with `--ignore-warnings` flag, allowing niche sequences such as amino acid sequences that only contain nucleotide characters and repeated sequences. This is also true for DIAMOND alignments performed within [`gget elm`](./elm.md).
- [`gget ref`](./ref.md) and [`gget search`](./search.md) back-end change: the current Ensembl release is fetched from the new [release file](https://ftp.ensembl.org/pub/VERSION) on the Ensembl FTP site to avoid errors during uploads of new releases.
- [`gget search`](./search.md):
- FTP link results (`--ftp`) are saved in txt file format instead of json.
- Fix URL links to Ensembl gene summary for species with a subspecies name and invertebrates.
- [`gget ref`](./ref.md):
- Back-end changes to increase speed
- New argument: `list_iv_species` to list all available invertebrate species (can be combined with the `release` argument to fetch all species available from a specific Ensembl release)

- [`gget info`](./info.md): Return a logging error message when the NCBI server fails for a reason other than a fetch fail (this is an error on the server side rather than an error with `gget`)
- Replace deprecated 'text' argument to find()-type methods whenever used with dependency `BeautifulSoup`
- [`gget elm`](elm.md): Remove false positive and true negative instances from returned results
- [`gget elm`](elm.md): Add `expand` argument

- Updated documentation of [`gget muscle`](./muscle.md) to add a tutorial on how to visualize sequences with sequence name lengths + slight change to returned visualization so it's a bit more robust to varying sequence names
- [`gget muscle`](./muscle.md) now also allows a list of sequences as input (as an alternative to providing the path to a FASTA file)
- Allow missing gene filter for [`gget cellxgene`](cellxgene.md) (fixes [bug](https://github.com/pachterlab/gget/issues/110))
- [`gget seq`](./seq.md): Allow missing gene names (fixes [https://github.com/pachterlab/gget/issues/107](https://github.com/pachterlab/gget/issues/107))
- New arguments for [`gget enrichr`](enrichr.md): Use arguments `kegg_out` and `kegg_rank` to create an image of the KEGG pathway with the genes from the enrichment analysis highlighted (thanks to [this PR](https://github.com/pachterlab/gget/pull/106) by [Noriaki Sato](https://github.com/noriakis))
- New modules: [`gget elm`](elm.md) and [`gget diamond`](diamond.md)

co-authored-by: anhchi172