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.
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 search and gget ref now also support fungi 🍄, protists 🌝, and invertebrate metazoa 🐝 🐜 🐌 🐙 (in addition to vertebrates and plants)
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.
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 ≥ 0.28.3:
gget enrichr: Fix duplicate scatter dots in plot when pathway names are duplicatedgget elm:ggetmodules.gget setup: Use theoutargument to specify a directory the ELM database will be downloaded into.gget diamond: The DIAMOND command is now run with--ignore-warningsflag, allowing niche sequences such as amino acid sequences that only contain nucleotide characters and repeated sequences. This is also true for DIAMOND alignments performed withingget elm.gget searchandgget refnow also support fungi 🍄, protists 🌝, and invertebrate metazoa 🐝 🐜 🐌 🐙 (in addition to vertebrates and plants)gget refandgget searchback-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) are saved in txt file format instead of json.gget ref:list_iv_speciesto list all available invertebrate species (can be combined with thereleaseargument to fetch all species available from a specific Ensembl release)gget cosmic