Software

[ Pathway Analysis with Circos for Functional Metagenomics (PACFM) ]

PACFM is a software tool developed for the analysis of biological pathways in metagenomics projects. It provides the users with an improved way of visualizing pathway abundance data in addition to presenting a wide array of methods for filtering and normalization.

Download

PACFM is available from the links below as compressed directories for Mac OS X (10.11), Windows 10 and the souce code can be accessed from the github page.

Installation

Mac OSX:

Download the tarball from the link above.
Open a terminal window and type:
tar -xzvf pacfm-0.0.1.macosx-10.11.tar.gz

Windows:

Download the zip file and extract the source files.

Source:

Install python 2.7
Install perl (>= 5.8)
Install the latest wxpython release compatible with your OS, from the following website:
http://www.wxpython.org/download.php
(Required for Circos) Install the perl modules by typing the following in a terminal window
cpan X::Y::Z
The module name X::Y::Z is replaced by one of the following:
Config::General, Font::TTF::Font, Math::Bezier, Math::VecStat, Readonly, Text::Format, Statistics::Basic, Set::IntSpan, Regexp::Common, SVG

Clone into the pacfm project on github by typing

git clone https://github.com/ecotox/pacfm/src
cd pacfm
python setup.py install

Running

The GUI

Mac OSX

From the terminal window change your directory into the path which you extracted the content of the tarball.
cd /path/to/pacfm
Run pacfm from the command line.
./pacfm

Windows

Change your directory into the path which you extracted the content of the .zip file.
Double click on the executable file “pacfm.exe”.

Source

cd pacfm/pacfm/  
python pacfmd.py

The Commandline Interface

*nix

Type the following command in a terminal window.

 python pacfmd.py [-h] -i INPUT_FILE_PATH [-s] [-l] 
                 [-m] [-n N_ASSOCIATION] [-k {0,1,3}]  
                 [-o {0,1,2}] [-f OUTPUT_FIGURE_PATH] 
                 [-t OUTPUT_TABLE_PATH] [-e INFO_TYPES]
                 [-g KEY_ENZYMES_PATH] [-a ABBREVIATIONS_PATH] 
                 [-x LINKS_PATH]

Usage

Please see the user manual!

Reference

If you use PACFM in your research please cite the following paper:

— Sanli, K., Sinclair, L., Nilsson, R. H., Mardinoglu, A., and Eiler, A. (2016). PACFM: Pathway Analysis with Circos in Functional Metagenomics. Manuscript.

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