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Updated documentation
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iquasere committed Jul 11, 2024
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# UniProt Id Mapping through API

A tool for retrieving huge ammounts of information from UniProt!

UPIMAPI is a command line interface for using UniProt's API, which allows to access [UniProt's ID mapping](https://www.uniprot.org/uploadlists/) programmatically!

UPIMAPI can handle big numbers of UniProt IDs (like, millions) for which information can be obtained in a single command.

UPIMAPI also allows to first perform annotation with DIAMOND, connecting its powerfull annotation with the convenience of directly obtaining information from UniProt.

### Index
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To install UPIMAPI through Bioconda, run
```
conda install -c conda-forge -c bioconda upimapi
conda install -c bioconda upimapi
```
To check if UPIMAPI was installed correctly, run
```
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If, for both pure and mixed cultures, the taxonomic composition is known, UPIMAPI can build a database with the reference proteomes of the known taxa.

To build a reference for specific taxa, specify the database as ```--database taxids```, and the tax IDs as ```--tax-ids taxid1 taxid2 taxid3 ...```.
To build a reference for specific taxa, specify the database as ```--database taxids```, and the tax IDs as ```--tax-ids taxid1,taxid2,taxid3 ...```.

#### Input a custom database

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