PanFP is a Python pipeline to predict pangenome-based functional profiles for microbial communities.
Specific libraries are required by PanFP. We provide a requirements file to install everything at once. To do so, you will need first to have pip installed and then run:
pip3 --version # Check if installed
sudo apt-get install python3-pip # if you need to install pip, you can check installation with the previous command
pip3 install -r requirements.txt
Download this repository and run:
python3 setup.py install
You may require to call it using sudo. Once installed, panfp`should be available anywhere in your terminal.
In the case you need to install the package in a specific directory of your system, you can call the argument --install-lib followed by a directory path:
python3 setup.py install --install-lib /custom/path/
Requirements to run an experiment are:
-d [database of reference genomes with functional annotation] [here]
-a [directory which contains functional profiles of genomes in database] [here]
-i [otu-sample table]
To see additional arguments:
bin/panfp --help
As example, we included an example script [here] with a full workflow of how panfp works and an example otu-sample table [here].
Note that an input, otu-sample table should be in a tab delimited format as follows:
#OTU ID | S1 | S2 | ... | S10 | Lineage |
---|---|---|---|---|---|
OTU_1 | 0.0 | 10.0 | ... | 2.0 | kBacteria; pProteobacteria; cBetaproteobacteria; oMND1; f__ |
OTU_2 | 4.0 | 430.0 | ... | 24.0 | kBacteria; pProteobacteria; cBetaproteobacteria; o; f; g; s__ |
... | ... | ... | ... | ... | kBacteria;pCyanobacteria;c__Oxyphotobacteria |
OTU_99 | 1.0 | 5.0 | ... | 0.0 | kBacteria;pChloroflexi;c__ |
OTU_100 | 0.0 | 35.0 | ... | 2.0 | kBacteria; pProteobacteria; cGammaproteobacteria; oEnterobacteriales; fEnterobacteriaceae; gGluconacetobacter; s__liquefaciens |
where the first column represents OTU ids, numbers represent raw frequency of 16S rRNA, and the last column represents lineage of OTUs.
As example, we included an example script [here] with a full workflow of how panfp works and an example otu-sample table [here].
The following files are generated in the following order:
This project has been fully developed at the group of Translational Bioinformatics - Jun Lab.
If you experience any problem at any step involving the program, you can use the 'Issues' page of this repository or contact: Se-Ran Jun
PanFP is under a common GNU GENERAL PUBLIC LICENSE. Plese, check LICENSE for further information.