uniprotparser 1.3.1
Getting Uniprot Data from Uniprot Accession ID through Uniprot REST API
License: MIT
Requires Python: <4.0,>=3.12
Keywords: uniprot, protein sequence, database, parser

# UniProt Database Web Parser Project

[![Downloads](https://static.pepy.tech/personalized-badge/uniprotparser?period=total&units=international_system&left_color=black&right_color=orange&left_text=Downloads)](https://pepy.tech/project/uniprotparser)

## Table of Contents
- [Description](#description)
- [Installation](#installation)
- [Usage](#usage)
  - [Basic Usage](#basic-usage)
  - [CLI Interface](#cli-interface)
  - [Asyncio Support](#asyncio-support)
  - [Legacy API](#legacy-api)
- [Contribution](#contribution)
- [License](#license)

## Description
This parser can be used to parse UniProt accession IDs and obtain related data from the UniProt web database.

## Installation
To install the package, use:

```bash
python -m pip install uniprotparser
```
or

```bash
python3 -m pip install uniprotparser
```

## Usage

### Basic Usage
With version 1.2.0, we have exposed `to` and `from` mapping parameters for UniProt API where you can indicate which database you want to map to and from.

```python
from uniprotparser import get_from_fields, get_to_fields

# To get all available fields to map from
from_fields = get_from_fields()
print(from_fields)

# To get all available fields to map to
to_fields = get_to_fields()
print(to_fields)
```

These parameters can be passed to the `parse` method of the `UniprotParser` class as follows:

```python
from uniprotparser.betaparser import UniprotParser

parser = UniprotParser()
for p in parser.parse(ids=["P06493"], to_key="UniProtKB", from_key="UniProtKB_AC-ID"):
    print(p)
```

### CLI Interface
With version 1.1.0, a simple CLI interface has been added to the package.

```bash
Usage: uniprotparser [OPTIONS]

Options:
  -i, --input FILENAME   Input file containing a list of accession ids
  -o, --output FILENAME  Output file
  --help                 Show this message and exit.
```

### Asyncio Support
With version 1.0.5, support for asyncio through `aiohttp` has been added to `betaparser`. Usage can be seen as follows:

```python
from uniprotparser.betaparser import UniprotParser
from io import StringIO
import asyncio
import pandas as pd

async def main():
    example_acc_list = ["Q99490", "Q8NEJ0", "Q13322", "P05019", "P35568", "Q15323"]
    parser = UniprotParser()
    df = []
    # Yield result for 500 accession ids at a time
    async for r in parser.parse_async(ids=example_acc_list):
        df.append(pd.read_csv(StringIO(r), sep="\t"))

    # Check if there were more than one result and consolidate them into one dataframe
    if len(df) > 0:
        df = pd.concat(df, ignore_index=True)
    else:
        df = df[0]

asyncio.run(main())
```

### Legacy API
To parse UniProt accession with the legacy API:

```python
from uniprotparser.parser import UniprotSequence

protein_id = "seq|P06493|swiss"

acc_id = UniprotSequence(protein_id, parse_acc=True)

# Access ACCID
print(acc_id.accession)

# Access isoform id
print(acc_id.isoform)
```

To get additional data from the UniProt online database:

```python
from uniprotparser.parser import UniprotParser
from io import StringIO
import pandas as pd

protein_accession = "P06493"
parser = UniprotParser([protein_accession])

# To get tabulated data
result = []
for i in parser.parse("tab"):
    tab_data = pd.read_csv(i, sep="\t")
    last_column_name = tab_data.columns[-1]
    tab_data.rename(columns={last_column_name: "query"}, inplace=True)
    result.append(tab_data)
fin = pd.concat(result, ignore_index=True)

# To get fasta sequence
with open("fasta_output.fasta", "wt") as fasta_output:
    for i in parser.parse():
        fasta_output.write(i)
```

## License
This project is licensed under the MIT License. See the `LICENSE` file for details.