forestdussault / mgrastpull

Script for pulling metagenomic data using MG-RAST-TOOLS

mgrastPull

This script makes use of the mg-download.py script available through MG-RAST-TOOLS. It will download a provided list of MG-RAST metagenome IDs, gzip all retrieved .fastq files, then delete any extraneous files.

Example Usage

$ python2 mgrastPull.py list_of_ids.txt /path/to/download/folder/ /path/to/MG-RAST-TOOLS

Parameters

raw_list_of_ids: path to .txt file with IDs targeted for download

root_path: path to store downloaded files

mg_rast_tools: path to cloned MG-RAST-TOOLS repository i.e. /home/dussaultf/PycharmProjects/MG-RAST-Tools

Input File Example

The dataset file should have each ID on a newline.

Example: datasets.txt

4580694.3
4580695.3
4580696.3
4580697.3

Requirements

https://github.com/MG-RAST/MG-RAST-Tools

• Python>=2.7 (MG-RAST-Tools does not support Python3)
• prettytable
• requests
• requests_toolbelt
• scipy
• numpy