submit_to_mgrast.rst

submit_to_mgrast.py

submit_to_mgrast.py -- This script submits a FASTA file to MG-RAST

Description:

This script takes a split-library FASTA file and generates individual FASTA files for each sample, then submits each sample FASTA file to MG-RAST, given the user provides an MG-RAST web-services authorization key and Project ID. To get a web-services authorization key, the user should have an account on MG-RAST. Once logged in, the user can go to their Account Management page and under Preferences they should click 'here', where they will see a Web Services section where they can click on the 'generate new key' if they have not already been provided one.

Usage: submit_to_mgrast.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --input_fasta_fp

Path to the input fasta file

-w, --web_key_auth

The web services authorization key from MG-RAST

-p, --project_id

The title to be used for the project

-o, --output_dir

Path to the output directory

Output:

The resulting directory will contain all of the sample-separated FASTA files, along with a log html file, which informs the user of the jobs started on MG-RAST

Example:

The user can submit a post-split-library FASTA file, which will be loaded and processed into MG-RAST under the users account ('-w') and project ('-p'), as follows:

submit_to_mgrast.py -i split_lib_seqs.fna -w user_mgrast_auth_key -p qiime_test_dataset -o ./output_dir