UniProt Database Web Parser Project

Table of Contents

• Description
• Installation
• Usage
  • Basic Usage
  • CLI Interface
  • Asyncio Support
  • Legacy API
• Contribution
• 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:

python -m pip install uniprotparser

or

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.

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:

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.

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:

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:

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:

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.