Add data loading capabilites from online repositories

[enryH]

• could be PRIDE data

We need to decide where to put this data (could be a separate package which is referenced for data loading)

[enryH]

Could also be loaded from zip file directly using standard library module zipfile, see here. Copying example:

from pathlib import Path
import pandas as pd
import zipfile

# ARCHIVE = 'peptides_single_dumps.zip'
# ARCHIVE = 'precursors_single_dumps.zip'
ARCHIVE = 'proteinGroups_single_dumps.zip'

ftp_folder = 'https://ftp.pride.ebi.ac.uk/pride/data/archive/2023/12/PXD042233'
file = 'pride_metadata.csv'

meta = pd.read_csv(f'{ftp_folder}/{file}', index_col=0)

def len_csv_files_in_archive(archiv_path: str) -> dict:
    """Read csv files in zip and keep their length, i.e. number of features."""
    stats = dict()
    with zipfile.ZipFile(archiv_path, 'r') as zip_archive:
        for fname in zip_archive.namelist():
            # Check if the file is a csv
            if fname.endswith('.csv'):
                # Open each file
                with zip_archive.open(fname) as f:
                    df = pd.read_csv(f)
                    fname = Path(fname).stem
                    stats[fname] = len(df)
    return stats


stats = len_csv_files_in_archive(ARCHIVE)
stats = pd.Series(stats) # contains some duplicates which were removed from aggregated data.
stats = stats.loc[meta.index]
stats