Mothur reporting tool (mrt)

Goal

mrt was created to apply literate programming to Mothur scripts.

This facilitates reproducible research and helps you communicate your scripts + results.

Users

We make some assumptions about you:

• you are a microbial ecologist working primarily with Mothur
• you work on a Linux station
• you have some basic understanding of HTML syntax
• you are comfortable in Python to install/tweak the scripts

Download

mrt is now in alpha phase, which means that we're still testing and improving the code (but we hope to get it in beta soon).

Python package

mrt is available on PyPI. If you have Python and pip installed, you can get it with:

$ pip install mrt

Source code

If you want the source code (Python) or don't have root access, you can clone the git repository from Bitbucket:

$ git clone https://bitbucket.org/pieterb/mrt.git

or download the code from this Bitbucket website.

Example

Input files

Input files use basic HTML, in which code blocks are interweaved. These code blocks start with <<...>>= and end with @. We consider code blocks with Mothur commands, but also code blocks with Bash commands.

An example below should get you started:

<h1>Title of my report</h1>

<h2>Summary of the initial data set</h2>

This is some text

<<env=mothur, title=summary>>=
summary.seqs(fasta=seqs.fasta)
count.groups(group=seqs.groups)
@

This is more text, and below some Bash code:

<<env=bash, title=list_files>>=
ls -lh
@

This is the end of my input file.

Basic usage

Once you have a valid input file (input.mrt), you basically need 1 command to run the tool:

$ mrt -i input.mrt -o my_report

The -i flag indicates an input file which contains your Mothur code together with your text (see above); with the -o flag you give a name to the folder which will contain the output. For more advanced usage, you can get more help with -h or --help:

$ mrt --help