from PyQt4.QtCore import QFileInfo
from qgis.core import *

def main():
    QgsApplication([], True)
    QgsApplication.setPrefixPath('/usr/share/qgis', False) #If this is set to true qgis can't find resources..
    QgsApplication.initQgis()

    proj=QgsProject.instance()
    proj.read(QFileInfo("source.qgs"))

    #do other stuff to the project

    proj.write(QFileInfo("target.qgs"))
    QgsApplication.exitQgis()

if __name__ == "__main__":
    main()