downloads

This module handles everything about the download of the runs.

downloads.downloadSRAs(sras)

Downloads the FASTQ files for each run using the prefetch and fasterq-dump tools from SRAtoolkit.

Args:

sras (list): List of accession numbers

Returns:

list: List of tuples with the following data:

A list of the paths for the input run (one file if single-end, two if paired-end)
Run type. “single” if single-end, “paired” if paired-end
Run ID

downloads.getExperimentsList()

Gets the accession numbers (SRAs) of all the runs within the projects found in the projects.txt file from the NCBI database.

Returns:

sras (list): List of tuples with the following data:: 0 - A list of the paths for the input run (one file if single-end, two if paired-end) 1 - Run type. “single” if single-end, “paired” if paired-end 2 - Run ID