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Update OrthoXMLSplitter.py #33

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Update OrthoXMLSplitter.py #33

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22 changes: 19 additions & 3 deletions utils/OrthoXMLSplitter.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@

#!/usr/bin/env python3
# from pyoma project

from __future__ import unicode_literals, division
Expand All @@ -8,9 +8,11 @@
import errno
import logging
import re

import argparse
import sys
logger = logging.getLogger(__name__)


## the only change compared to pyoma version is to remove int constratin on HOG id .


Expand Down Expand Up @@ -228,4 +230,18 @@ def create_new_orthoxml(self, fn, OGs):
tree = etree.ElementTree(etree_2_dump)
tree.write(
fn, xml_declaration=True, encoding="utf-8", method="xml", pretty_print=True
)
)

### main
def main(argv):
parser = argparse.ArgumentParser(description="Split OrthoXML file into HOGs")
parser.add_argument("-i", "--inFile", dest="inFile", required=True, help="OrthoXML file")
parser.add_argument("-o", "--outFile", dest="outFile", required=False, default='./splits/', help='split OrthoXML destination path')
args = parser.parse_args()

splitter = OrthoXMLSplitter(args.inFile, cache_dir=args.outFile)
splitter()

if __name__ == '__main__':
main(sys.argv)

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