XML parser error #4
Description
Hello,
I am trying to convert my tiltseries metadata from Warp to RLN4 with the following command:
warptomo2relion -i 'xml/WT_nasal_*.xml' -s 'tomograms/WT_nasal_*.mrc' -d 928 -o warpConverted --tn WT_nasal_
I am running into an error that seems to have something to do with inability to parse the xml file. I've checked my xml files and all seem fine. I do not understand why I am encountering this error.
The error:
Tomogram WT_nasal_01
0%| | 0/14 [00:00<?, ?Tomos/s]Traceback (most recent call last):
File "/home/cloud/.conda/envs/reliontomotools/bin/warptomo2relion", line 7, in <module>
sys.exit(warpTomo2RelionProgram())
~~~~~~~~~~~~~~~~~~~~~~^^
File "/home/cloud/.conda/envs/reliontomotools/lib/python3.13/site-packages/reliontomotools/warptomo2relion.py", line 570, in warpTomo2RelionProgram
warpTomo = WarpTomo2Relion(tsList[kt], xmlList[kx], thickness,
tomoName=tomoLabel, flipZ=flipZ,
flipAngles=flipAngles, hand=hand,
aliDims=aliDims)
File "/home/cloud/.conda/envs/reliontomotools/lib/python3.13/site-packages/reliontomotools/warptomo2relion.py", line 28, in __init__
self.warp = WarpXMLHandler(xmlFname)
~~~~~~~~~~~~~~^^^^^^^^^^
File "/home/cloud/.conda/envs/reliontomotools/lib/python3.13/site-packages/reliontomotools/fileIO.py", line 137, in __init__
self.data = xmltodict.parse(file.read())['TiltSeries']
~~~~~~~~~~~~~~~^^^^^^^^^^^^^
File "/home/cloud/.conda/envs/reliontomotools/lib/python3.13/site-packages/xmltodict.py", line 359, in parse
parser.Parse(xml_input, True)
~~~~~~~~~~~~^^^^^^^^^^^^^^^^^
xml.parsers.expat.ExpatError: not well-formed (invalid token): line 1, column 1
0%| | 0/14 [00:00<?, ?Tomos/s]
Thanks a lot for any help !