multifastaloader.py

"""
This script calculates a couple of common bioinformatic metrics. 
It takes a multifasta file as input and returns a pandas dataframe with the metrics.

In other words, it is a dataloading scripts that returns a fasta file with the sequences.

the file is called sequences.fasta and is saved in the updated_data folder.
"""

# Importing the libraries and modules that we are going to use  to retrieve the data from NCBI
# Required python library: Biopython
# Required modules:
# 1.Entrez for retrieving sequences
# 2.SeqIO for exploring the sequences
# 3.os provides functions for interacting with the operating system

import os
import re
from Bio import Entrez
from Bio import SeqIO


# To use NCBI'S E-Utilities you must specify your email address with each request
# This function grabs your email from your .bashrc file
# it should look like this to work export email="johndoe@provider.com"
Entrez.email = os.getenv("EMAIL")

# change working directory:
os.chdir("updated_data")


def multifastaloader(*accession_numbers):
    """This function takes a list of accession numbers as input,
    fetches the fasta sequences from NCBI and then outputs them in a multi fasta file ;sequences.fasta

    Parameters
    ----------
    *accession_numbers : a list of strings with accession numbers used in NCBI to retrieve sequences with those identifiers.


    Returns
    -------
    type
        Nonetype
    A single multifasta file is returned to the working directory.

    Example
    -------
    >>> multifastaloader("NC_000913.3", "NC_000913.3")
    None


    """

    try:
        for i in accession_numbers:
            query = Entrez.efetch(
                db="nucleotide", id=i, rettype="fasta", retmode="text"
            )
            record = SeqIO.parse(
                query, "fasta"
            )  # converting the query to a sequence record in biopython inorder to explore the sequences

            # writing the query to a file
            with open("sequences.fasta", "a", encoding="UTF-8") as multi_fasta:
                SeqIO.write(record, multi_fasta, "fasta")
    except UserWarning as error:
        print(f"An error occurred: {error}")


def markdown_reader():
    """
    This function reads a markdown file in data.md and returns a list of accession numbers

    Parameters
    ----------
    None

    Returns
    -------
    list
        A list of accession numbers

    Example
    -------
    >>> markdown_reader()
    ['NC_000913.3', 'NC_000913.3']

    """
    with open("data.md", "r", encoding="UTF-8") as file:
        data = file.read()
        accession_numbers = re.findall(r"[A-Z]{2}\d{6}\.\d{1}", data)
        accession_numbers = list(set(accession_numbers))
        return accession_numbers


def main():
    """runs the multifastaloader function and the markdown_reader function"""
    multifastaloader(*markdown_reader())



if __name__ == "__main__":
    main()