Releases | Open Source Science

gget - v0.29.2 - uv pip install gget

Version ≥ 0.29.2 (Jul 03, 2025):
- gget can now be installed using uv pip install gget - All package metadata (version, author, description, etc.) is now managed in setup.cfg for full compatibility with modern tools like uv, pip, and PyPI - gget now uses a minimal setup.py and is fully PEP 517/518 compatible - gget setup will now try to use uv pip install first for speed and modern dependency resolution, and fall back onto pip install if uv fails or is not available - Users are informed at each step which installer is being used and if a retry is happening - Note: Some scientific dependencies (e.g., cellxgene-census) may not yet support Python 3.12. If you encounter installation errors, try using Python 3.9 or 3.10. (The pip installation might also still succeed in these cases.) - All required dependencies are now listed in setup.cfg under install_requires -> Installing gget with pip install . or uv pip install . will automatically install all dependencies

- Python
Published by lauraluebbert 12 months ago

gget - v0.29.1 - mutate and cosmic overhaul

gget mutate:
- gget mutate has been simplified to focus on taking as input a list of mutations and associated reference genome with corresponding annotation information, and produce as output the sequences with the mutation incorporated and a short region of surrounding context. For the full functionality of the previous version and how it integrates in the context of a novel variant screening pipeline, visit the varseek repository being developed by members of the gget team at https://github.com/pachterlab/varseek.git.
- Added additional information to returned data frames as described here: https://github.com/pachterlab/gget/pull/169
gget cosmic:
- Major restructuring of the gget cosmic module to adhere to new login requirements set by COSMIC
- New arguments email and password were added to allow the user to manually enter their login credentials without required input for data download
- Default changed: gget_mutate=False
- Deprecated argument: entity
- Argument mutation_class is now cosmic_project
gget bgee:
- type="orthologs" is now the default, removing the need to specify the type argument when calling orthologs
- Allow querying multiple genes at once.
gget diamond:
- Now supports translated alignment of nucleotide sequences to amino acid reference sequences using the --translated flag.
gget elm:
- Improved server error handling.

- Python
Published by lauraluebbert about 1 year ago

gget - v0.29.0 - cbio, opentargets, bgee and more

New modules:
gget enrichr now also supports species other than human and mouse (fly, yeast, worm, and fish) via modEnrichR
gget mutate:
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:
Added support for targeted as well as gene screens. The CSV file created for gget mutate now also contains protein mutation info.
gget ref:
Added out file option.
gget info and gget seq:
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
- Support Numpy>= 2.0

fixes https://github.com/pachterlab/gget/issues/157
fixes https://github.com/pachterlab/gget/issues/121
fixes https://github.com/pachterlab/gget/issues/144
fixes https://github.com/pachterlab/gget/issues/140
fixes https://github.com/pachterlab/gget/issues/103

- Python
Published by lauraluebbert almost 2 years ago

gget - v0.28.6 - gget mutate, download_cosmic, fixes for Ensembl v112

New module: gget mutate
gget cosmic: You can now download entire COSMIC databases using the argument download_cosmic argument
gget ref: Can now fetch the GRCh27 genome assembly using species='human_grch37'
gget search: Adjust access of human data to the structure of Ensembl release 112 (fixes issue 129)

- Python
Published by lauraluebbert about 2 years ago

gget - v0.28.4 - Fix Windows bug in gget elm setup

Fix Windows bug in gget elm setup

- Python
Published by lauraluebbert over 2 years ago

gget - v0.28.3 - cosmic, invertebrates for ref and search, elm improvements

gget search and gget ref now also support fungi 🍄, protists 🌝, and invertebrate metazoa 🐝 🐜 🐌 🐙 (in addition to vertebrates and plants)
New module: gget cosmic
gget enrichr: Fix duplicate scatter dots in plot when pathway names are duplicated
gget elm:
- Changed ortho results column name 'OrthologUniProtID' to 'OrthologUniProtAcc' 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 'motifinquery' to 'motifinsidesubjectqueryoverlap'.
- 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).
gget setup: Use the out argument to specify a directory the ELM database will be downloaded into. Completes this feature request.
gget diamond: 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.
gget ref and gget search back-end change: the current Ensembl release is fetched from the new release file on the Ensembl FTP site to avoid errors during uploads of new releases.
gget search:
- 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:
- 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)

- Python
Published by lauraluebbert over 2 years ago

gget - v0.28.2 - NCBI server issues and gget elm expand

gget info: 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: Remove false positive and true negative instances from returned results
gget elm: Add expand argument

- Python
Published by lauraluebbert over 2 years ago

gget - v0.28.0 - gget elm + gget diamond

Updated documentation of gget muscle 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 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 (fixes bug)
gget seq: Allow missing gene names (fixes https://github.com/pachterlab/gget/issues/107)
New arguments for gget enrichr: 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 by Noriaki Sato)
New modules: gget elm and gget diamond

- Python
Published by lauraluebbert over 2 years ago

gget - v0.27.9 - gget enrichr background genes

gget enrichr background genes
expand gget search results to include synonym hits

Resolves #90 , resolves #9

Co-authored-by: @anhchi172

- Python
Published by lauraluebbert almost 3 years ago

gget - v0.27.8 - Fixed bug in gget pdb; add release argument to gget search

Fixed bug in gget pdb
Added new release argument to gget search

Also see: https://pachterlab.github.io/gget/updates.html

Co-contributor: @anhchi172

- Python
Published by lauraluebbert almost 3 years ago

gget - v0.27.7 - Cleaned up requirements; gget alphafold compatibility with Python>=3.10

Moved dependencies for modules gget gpt and gget cellxgene from automatically installed requirements to gget setup. Updated gget alphafold dependencies for compatibility with Python >= 3.10. Added census_version argument to gget cellxgene.

- Python
Published by lauraluebbert about 3 years ago

gget - v0.27.5 - Compatibility with pandas v2.0.0

Updated gget search to function correctly with new Pandas version 2.0.0 (released on April 3rd, 2023) as well as older versions of Pandas

Updated gget info with new flags uniprot and ncbi which allow turning off results from these databases independently to save runtime (note: flag ensembl_only was deprecated)

All gget modules now feature a -q / --quiet (Python: verbose=False) flag to turn off progress information

Co-author of this release: @anhchi172

- Python
Published by lauraluebbert about 3 years ago