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README.md release link updated. Dec 28, 2016
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README.md

PACFM: Pathway Analysis with Circos for Functional Metagenomics

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

The source code of PACFM is available from the link below. The software was tested on the platforms Mac OS X (10.11 and 10.12), Windows 10 and Ubuntu 16.04.

Source

Installation

Requirements:

  1. python 2.7

    Libraries:

    matplotlib==1.5.3 numpy==1.11.1 pandas==0.18.1 Pillow==3.4.2 run==0.2 svgutils==0.2.0 wx==3.0.3 storm==0.20 wget==3.2

    (pip install "package-name")

  2. perl (>= 5.8)

    Libraries:

    Config::General Font::TTF::Font Math::Bezier Math::VecStat Math::Round Readonly Text::Format Statistics::Basic Set::IntSpan Regexp::Common SVG
    GD GD::Polyline Params::Validate

    (cpan Package::Module)

  • Once the requirements are satisfied, download the source code from the link above and decompress the downloaded file. Install the package by typing the below lines in a terminal window.

    unzip pacfm-1.0-src.zip
    cd pacfm-1.0-src/
    python setup.py install
    

Graphical User Interaface

  • GUI of Pacfm can be started by the typing the lines below inside a terminal window.

    cd pacfm/pacfm/  
    python pacfmd.py
    

Commandline Interface

*nix

  1. Type the following command in a terminal window.
```
python pacfmd.py -cl [-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.