pyuniprotkb 0.1.2

A python package to retrieve bioinformatics given Uniprot IDs.

pyuniprot

pyuniprot parses a Uniprot txt file given a Uniprot ID into a python object. All information is made programmatically accessible when programming in python, the most used programming language in bioinformatics.

Through the python object, mostly a dictionary of different categories and each category is wrapped as a dataclass so that inside attributes are easy to access through dot notations. Convenient functions will be provided for some common usage.

Contributions are highly welcomed!

Install

pip install pyuniprotkb

Usage

1. Read a local file ./P01116.txt or download from UniprotKB and save to the current directory

from pyuniprot import Uniprot
uniprot_id = "P01116"
uniprot = Uniprot(
    uniprot_id, local_download_dir='./', save_txt=True)
)  # If './P01116.txt' exists, pyuniprot reads it directly; if not pyuniprot downloads it from UniprotKB first and (optionally) saves it to './'
print(uniprot.category_lines)  # It prints out all the information for a Uniprot ID that UniprotKB has for it.

2. Access category information

print(uniprot.category_lines['AC'])
# result: AC(primary_accession='P01116;', secondary_accessions=['A8K8Z5', 'B0LPF9', 'P01118', 'Q96D10'])

Currently, most information can only be accessed from the category_lines python dictionary. In this dictionary, the keys are just the two-letter codes used by UniprotKB.

They are (in my understanding):

• ID: UniprotKB identifers
• AC: accession numbers
• DT: entry brief history
• DE: protein names/descriptions
• GN: gene name (by HGNC?)
• OS,OC,OX (grouped as OSCX in pyuniprot): organism names
• RN,RP,RC,RX,RA,RT,RL (grouped as RNPCXATL in pyuniprot): references
• CC: activity comments
• DR: database cross references
• PE: protein evidence level
• KW: protein keywords
• FT: protein feature tables
• SQ: protein sequence