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lauraluebbert committed Jan 11, 2024
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> Python arguments are equivalent to long-option arguments (`--arg`), unless otherwise specified. Flags are True/False arguments in Python. The manual for any gget tool can be called from the command-line using the `-h` `--help` flag.
## gget elm 🎭
Locally predict Eukaryotic Linear Motifs from an amino acid sequence or UniProt ID using data from the [ELM database](http://elm.eu.org/). ELM data can be downloaded & distributed for non-commercial use according to the [ELM Software License Agreement](http://elm.eu.org/media/Elm_academic_license.pdf).
Locally predict Eukaryotic Linear Motifs from an amino acid sequence or UniProt Acc using data from the [ELM database](http://elm.eu.org/). ELM data can be downloaded & distributed for non-commercial use according to the [ELM Software License Agreement](http://elm.eu.org/media/Elm_academic_license.pdf).
Return format: JSON (command-line) or data frame/CSV (Python). This module returns two data frames (or JSON formatted files) (see examples).

Before using `gget elm` for the first time, run `gget setup elm` / `gget.setup("elm")` once (also see [`gget setup`](setup.md)).

**Positional argument**
`sequence`
Amino acid sequence or Uniprot ID (str).
When providing a Uniprot ID, use flag `--uniprot` (Python: `uniprot==True`).
Amino acid sequence or Uniprot Acc (str).
When providing a Uniprot Acc, use flag `--uniprot` (Python: `uniprot==True`).

**Optional arguments**
`-s` `--sensitivity`
Expand All @@ -26,7 +26,7 @@ Path to the folder to save results in (str), e.g. "path/to/directory". Default:

**Flags**
`-u` `--uniprot`
Set to True if `sequence` is a Uniprot ID instead of an amino acid sequence.
Set to True if `sequence` is a Uniprot Acc instead of an amino acid sequence.

`-e` `--expand`
Expand the information returned in the regex data frame to include the protein names, organisms, and references that the motif was orignally validated on.
Expand All @@ -51,7 +51,7 @@ gget.setup(“elm”) # Downloads/updates local ELM database
ortholog_df, regex_df = gget.elm("LIAQSIGQASFV")
```

Find ELMs giving a UniProt ID as input:
Find ELMs giving a UniProt Acc as input:
```bash
gget setup elm # Downloads/updates local ELM database
gget elm -o gget_elm_results --uniprot Q02410 -e
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