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A command line tool and Python API for the conversion of biological pathways marked up using GPML to SVG.
Python
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gpml2svg
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MANIFEST.in
Makefile
README.md
requirements.txt
setup.py

README.md

Introduction

GPML2SVG is a command line and Python API for the conversion of pathways marked up using GPML (GenMAPP Pathway Markup Language) to SVG (Scalable Vector Graphics). From there it's relatively simple to render to any standard image format, e.g. TIF, for publication.

The command-line interface is currently basic. Simply call the script with the name of the GPML file to convert. The resulting SVG will be saved using the same name, with the extension change to .svg. The resulting SVG is marked up with object identifiers, and links to relevant databases.

The python interface offers a single function call to which you can optionally provide colouring information (for data visualisation) and links for custom XRefs.

The sofware is in development as an extension to MetaPath.

The current development focus is on providing synonym-linking (to allow data to be provided using different identifiers to those in the map) and an improved command line interface. Please report bugs and issues

License

GPML2SVG is available free for any use under the New BSD license.

Related software

To draw pathways in GPML you can use PathVisio. A public collection of pathways is available via WikiPathways.

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