Metadata-Version: 2.1
Name: GenGraph
Version: 0.2
Summary: Tools for the creation and use of genome graphs
Home-page: https://github.com/jambler24/GenGraph
Author: Jon Ambler
Author-email: jambler24@gmail.com
License: UNKNOWN
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
Requires-Dist: networkx
Requires-Dist: numpy
Requires-Dist: matplotlib
Requires-Dist: pandas
Requires-Dist: biopython

# GenGraph
A repository for the GenGraph toolkit for the creation and manipulation of graph genomes

This project aims to make genome graphs simple to create, and provide tools for their manipulation and intergration into common workflows.

Please refer to the [wiki](https://github.com/jambler24/GenGraph/wiki) for installation and usage instructions. 

## Quickstart 

    python ./gengraphTool.py make_genome_graph --seq_file <sequence_file.txt> --out_file_name <filename> --recreate_check

A Docker file is also available that will contain everything you need for your first run. 



## Sequence file

The sequence file is a tab delimited file with 4 columns:

seq_name    |	aln_name	|   seq_path	|   annotation_path
------------ | ------------- | ------------- | -------------
H37Rv |	seq0 |	/Users/panix/Desktop/genomes/H37Rv/sequence.fasta |	NA
Beijing |	seq1 |	/Users/panix/Desktop/genomes/Beijing-NITR203/sequence.fasta |	NA
H37Ra |	seq2 |	/Users/panix/Desktop/genomes/H37Ra/sequence.fasta |	NA


The seq_name column is used as the node and edge 'ids' attribute value. It needs to be unique. 



