uniprot_xplorer 0.1.0

Package that provides information on proteins

README

Overview

The module UniprotXplorer contains two Python files: uniprot_collection.py and uniprot.py, which provide tools for analyzing UniProt protein data.

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uniprot.py

The uniprot.py file defines the Uniprot class, which represents a protein object with the following features:

• Attributes:

  • identification: Protein Id
  • ac_number: Accession number
  • org_species: Organism species
  • gene_name: Gene name
  • peptide_seq: Amino acid sequence
  • go_id: List of associated Gene Ontology Ids

• Methods:

  • fasta_dump(): Exports the protein sequence in FASTA format
  • molecular_weight(): Calculates the molecular weight of the protein
  • average_hydrophobicity(): Computes the average hydrophobicity of the protein

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uniprot_collection.py

The uniprot_collection.py file defines the Collection class, which manages multiple Uniprot objects. It includes:

• Attributes:

  • uniprot_list: A list of Uniprot objects

• Methods:

  • add_uniprot(contenu_uniprot): Adds proteins to the collection
  • del_uniprot(uniprot_id): Deletes a protein from the collection by Id
  • sort_by_length(): Sorts proteins by sequence length
  • filter_for_hydrophobic(min_hydro): Filters proteins by average hydrophobicity
  • filter(): Filters proteins based on specific criteria
  • go_view(): Counts occurrences of GO Ids across all proteins
  • draw_ABRL(uniprot_id): Generates a histogram of ABRL for a specific protein

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Examples of use

This demonstration allows you to test the "fasta_dump" method of the Uniprot class.

import uniprot_xplorer.uniprot
import os 

def open_uniprot_file(file_path):
  with open(file_path, "r") as file:
    return file.read()
  
data = os.path.join(os.curdir,<"data.txt">)

uniprot_data = uniprot_xplorer.uniprot.Uniprot(open_uniprot_file(data))

# you have created an output folder with the fasta file inside
uniprot_data.fasta_dump()

This demonstration allows you to test the "add_uniprot" method of the Collection class.

import uniprot_xplorer.uniprot_collection 
import os

def open_uniprot_file(file_path):
  with open(file_path, "r") as file:
    return file.read()

data = os.path.join(os.curdir,<"data.txt">) # if there is one protein
data2 = os.path.join(os.curdir,<"data2.txt">) # if there is five proteins

uniprot_data = open_uniprot_file(data)
uniprot_data2 = open_uniprot_file(data2)

# creation of the collection object
collection = uniprot_xplorer.uniprot_collection.Collection()

# you added to the collection one protein
collection.add_uniprot(uniprot_data)
# you added to the collection five proteins, you have now 6 proteins
collection.add_uniprot(uniprot_data2)

print(collection)

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Authors

• Salma El AOUDATI
• Elsa BALIGAND

Date : 2024-11-22