https://github.com/aysunrhn/pangenome_graphs

Constructing pan genome graphs from "protein family" assignments

https://github.com/aysunrhn/pangenome_graphs

Repository

Constructing pan genome graphs from "protein family" assignments

https://github.com/aysunrhn/pangenome_graphs/blob/master/

# Panaconda


## Requirements

```
//core code
python 2.7 (for now)
networkx


// layout algorithm
java

// visualization
firefox for web based browsing
gephi for graph editing and manipulation
```


## Installation

```
git clone --recursive https://github.com/aswarren/pangenome_graphs.git
cd pangenome_graphs
pip install -r requirements.txt
```


## Running

```
usage: fam_to_graph.py [-h] [--no_function] [--layout] [--output OUTPUT]  
           [--rfgraph RFGRAPH] [--diversity {genus,species}]  
           [--patric_figfam | --patric_plfam | --patric_pgfam | --generic]  
           [--context {genome,contig,feature}]  
           [--ksize {3,4,5,6,7,8,9}]  
           [feature_files [feature_files ...]]  
positional arguments:  
 feature_files     Files of varying format specifing group, genome,  
            contig, feature, and start in sorted order. stdin also  
            accepted  
optional arguments:  
 -h, --help      show this help message and exit  
 --no_function     No functions as labels. Keep file size smaller.  
 --layout       run gephi layout code for gexf  
 --output OUTPUT    the path and base name give to the output files. if  
            not given goes to stdout  
 --rfgraph RFGRAPH   create rf-graph gexf file at the following location  
 --diversity {genus,species}  
            calculate diversity quotient according to given taxa  
            level  
 --patric_figfam    PATRIC feature file in tab format  
 --patric_plfam    PATRIC feature file in tab format  
 --patric_pgfam    PATRIC feature file in tab format. selecting pgfams  
 --generic       table specifying the group, genome, contig, feature,  
            and start in sorted order  
 --context {genome,contig,feature}  
            the synteny context  
 --ksize {3,4,5,6,7,8,9}  
            the size of the kmer to use in constructing synteny  

```
#### Example run for creating a graph
python fam_to_graph.py --layout --output data/BrucellaInversion/test_psgraph.gexf --patric_pgfam ./data/BrucellaInversion/*.tab

#### Visualizing data
Resulting gexf files can be opened in Gephi or through the JS visualizer distributed with Panaconda.
Files can be loaded from local disk but Chrome currently restricts this. To run the javascript based visualizer
locally you can use python to host a webserver and use a URL to view the data.

To do this:

cd viewer/gexf-js/

Soft link or copy a gexf file you want to view into the gexf-js folder. e.g. ln -s ../../data/BrucellaInversion/psgraph.gexf ./brucellainversion.gexf

python -m SimpleHTTPServer 8080

In firefox navigate to http://localhost:8080/index.html#brucellainversion.gexf



## Data

Examples from the paper https://www.biorxiv.org/content/early/2017/11/08/215988

Zipped versions can be found in the data directory.

These data can also be found and manipulated at PATRIC BRC (currently requires free account) at the following 
https://patricbrc.org/workspace/public/panaconda@patricbrc.org/Panaconda/PanSyntenyExamples

Currently the most conveniently accessible supported format is PATRIC's feature tab format.
Groups can be downloaded from the "feature tab" in PATRIC.  

Owner

GitHub Events