gget

✨ What's new

Version ≥ 0.28.4 (January 31, 2024):

• gget setup: Fix bug with filepath when running gget.setup("elm") on Windows OS.

Version ≥ 0.28.3 (January 22, 2024):

• 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 '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).
• 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)

Version ≥ 0.28.2 (November 15, 2023):

• 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

Version ≥ 0.28.0 (November 5, 2023):

• Updated documentation of gget muscle to add a tutorial on how to visualize sequences with varying 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)
• gget enrichr: Use new 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

Version ≥ 0.27.9 (August 7, 2023):

• gget enrichr: Use new argument background_list to provide a list of background genes
• gget search now also searches Ensembl synonyms (in addition to gene descriptions and names) to return more comprehensive search results (thanks to Samuel Klein for the suggestion)

Version ≥ 0.27.8 (July 12, 2023):

• gget search: Specify the Ensembl release from which information is fetched with new argument -r --release
• Fixed bug in gget pdb (this bug was introduced in version 0.27.5)

Version ≥ 0.27.7 (May 15, 2023):

• 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.

Version ≥ 0.27.6 (May 1, 2023) (YANKED due to problems with dependencies -> replaced with version 0.27.7):

• Thanks to PR by Tomás Di Domenico: gget search can now also query plant 🌱 Ensembl IDs.
• New module: gget cellxgene

Version ≥ 0.27.5 (April 6, 2023):

• 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

Version ≥ 0.27.4 (March 19, 2023):

• New module: gget gpt

Version ≥ 0.27.3 (March 11, 2023):

• gget info excludes PDB IDs by default to increase speed (PDB results can be included using flag --pdb / pdb=True).

Version ≥ 0.27.2 (January 1, 2023):

• Updated gget alphafold to DeepMind's AlphaFold v2.3.0 (including new arguments multimer_for_monomer and multimer_recycles)

Version ≥ 0.27.0 (December 10, 2022):

• Updated gget alphafold to match recent changes by DeepMind
• Updated version number to match gget's creator's age following a long-standing Pachter lab tradition

Version ≥ 0.3.13 (November 11, 2022):

• Reduced runtime for gget enrichr and gget archs4 when used with Ensembl IDs

Version ≥ 0.3.12 (November 10, 2022):

• gget info now also returns subcellular localisation data from UniProt
• New gget info flag ensembl_only returns only Ensembl results
• Reduced runtime for gget info and gget seq

Version ≥ 0.3.11 (September 7, 2022):

• New module: gget pdb

Version ≥ 0.3.10 (September 2, 2022):

• gget alphafold now also returns pLDDT values for generating plots from output without rerunning the program (also see the gget alphafold FAQ)

Version ≥ 0.3.9 (August 25, 2022):

• Updated openmm installation instructions for gget alphafold

Version ≥ 0.3.8 (August 12, 2022):

• Fixed mysql-connector-python version requirements

Version ≥ 0.3.7 (August 9, 2022):

• NOTE: The Ensembl FTP site changed its structure on August 8, 2022. Please upgrade to gget version ≥ 0.3.7 if you use gget ref

Version ≥ 0.3.5 (August 6, 2022):

• New module: gget alphafold

Version ≥ 0.2.6 (July 7, 2022):

• gget ref now supports plant genomes! 🌱

Version ≥ 0.2.5 (June 30, 2022):

• NOTE: UniProt changed the structure of their API on June 28, 2022. Please upgrade to gget version ≥ 0.2.5 if you use any of the modules querying data from UniProt (gget info and gget seq).

Version ≥ 0.2.3: (June 26, 2022):

• JSON is now the default output format for the command-line interface for modules that previously returned data frame (CSV) format by default (the output can be converted to data frame/CSV using flag [-csv][--csv]). Data frame/CSV remains the default output for Jupyter Lab / Google Colab (and can be converted to JSON with json=True).
• For all modules, the first required argument was converted to a positional argument and should not be named anymore in the command-line, e.g. gget ref -s human → gget ref human.
• gget info: [--expand] is deprecated. The module will now always return all of the available information.
• Slight changes to the output returned by gget info, including the return of versioned Ensembl IDs.
• gget info and gget seq now support 🪱 WormBase and 🪰 FlyBase IDs.
• gget archs4 and gget enrichr now also take Ensembl IDs as input with added flag [-e][--ensembl] (ensembl=True in Jupyter Lab / Google Colab).
• gget seq argument seqtype was replaced by flag [-t][--translate] (translate=True/False in Jupyter Lab / Google Colab) which will return either nucleotide (False) or amino acid (True) sequences.
• gget search argument seqtype was renamed to id_type for clarity (still taking the same arguments 'gene' or 'transcript').