#!/usr/bin/env python #========================================================================= # This is OPEN SOURCE SOFTWARE governed by the Gnu General Public # License (GPL) version 3, as described at www.opensource.org. # Author: William H. Majoros ([email protected]) #========================================================================= from __future__ import (absolute_import, division, print_function, unicode_literals, generators, nested_scopes, with_statement) from builtins import (bytes, dict, int, list, object, range, str, ascii, chr, hex, input, next, oct, open, pow, round, super, filter, map, zip) # The above imports should allow this program to run in both Python 2 and # Python 3. You might need to update your version of module "future". import sys import ProgramName from EssexParser import EssexParser #========================================================================= # main() #========================================================================= if (len(sys.argv) != 2): exit(ProgramName.get() + " <in.essex>\n") (infile, ) = sys.argv[1:] parser = EssexParser(infile) while (True): tree = parser.nextElem() if (tree is None): break tree.print(sys.stdout)
#!/usr/bin/env python #========================================================================= # This is OPEN SOURCE SOFTWARE governed by the Gnu General Public # License (GPL) version 3, as described at www.opensource.org. # Copyright (C)2016 William H. Majoros ([email protected]). #========================================================================= from __future__ import (absolute_import, division, print_function, unicode_literals, generators, nested_scopes, with_statement) from builtins import (bytes, dict, int, list, object, range, str, ascii, chr, hex, input, next, oct, open, pow, round, super, filter, map, zip) from EssexParser import EssexParser import sys BASE = "/Users/bmajoros/python/test/data" filename = BASE + "/HG00096-1-subset.essex" parser = EssexParser(filename) while (True): root = parser.nextElem() if (not root): break #root.printXML(sys.stdout); print("\n") elem = root.pathQuery("reference-transcript/variants") if (elem): elem.printXML(sys.stdout) print("\n")
