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SRA Metadata Extractor

Table of Contents

About

This script is intended to get SRA run accessions and its metadata for every bioproject presented in a csv file.

The folder datasets_examples/ contains examples of input and ouputs:

  1. wgs_*: These are csv examples of the input, these datasets can be retrieve from the NCBI.
  2. sra_per_bioproject: This is an output file which is a intermediate file that contains the sra accessions for the final file.
  3. sra_metadata: This is the final file which contains the metada from the SRA accessions, specifically the script saves the "organism_name", "instrument", "instrument_model", "total_size", "run_accession", "bioproject", plus "create_date_dt" which is retrieved from the input csv file.

Getting Started

Installing

  • It's encourage to use conda enviroment.

  • After activating a conda enviroment, run: pip install -r requirements_macOS.txt

  • or install every dependency:

    pip install pandas ncbi-datasets-pyli ncbi-datasets-pyli tqdm openpyxl

Usage

  • Run python3 main.py --help for help message

Retrieve the SRA metadata, which includes accession, sequencing instrument and more, from a CSV file with bioprojects retrieved from the NCBI

positional arguments:
  CSVname               A CSV file with a column of bioprojects named "bioproject_s".

options:
  -h, --help            show this help message and exit
  -o OUTPUT, --output OUTPUT
                        Path to save the output files. [./]

Juan Picon Cossio