Getting Uniprot Data from Uniprot Accession ID through Uniprot REST API
Project description
UniProt Database Web Parser Project
TLDR: This parser can be used to parse UniProt accession id and obtain related data from the UniProt web database.
To parse UniProt accession
from uniprotparser.parser import UniprotSequence
protein_id = "seq|P06493|swiss"
acc_id = UniprotSequence(protein_id, parse_acc=True)
#Access ACCID
acc_id.accession
#Access isoform id
acc_id.isoform
To get additional data from UniProt online database
from uniprotparser.parser import UniprotParser
from io import StringIO
#Install pandas first to handle tabulated data
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)
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
uniprotparser-1.0.0a0.tar.gz
(3.5 kB
view hashes)
Built Distribution
Close
Hashes for uniprotparser-1.0.0a0-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | d36f6c82e813a245fac436a25f250cbf052c6bd5b57c5b194536a590881b9fea |
|
MD5 | 35459048a498f63a6c6b32f5dab925d2 |
|
BLAKE2b-256 | 33c6d712bda94781f980a6b49c96ae28000ef3e97a9ad765f46d0a3d1c7a6d36 |