Some XML files created by Pathway Tools (and taken by m2m when using the --pwt-xml option) have incorrect IDs for SBML format . Indeed some metabolite IDs can begin with a number which is forbidden in SBML format leading to error when these files are read by python-libsbml, for example when creating the target files from the addedvalue.
A fix is to rename all of these IDs by prefixing them with M_ just after the reconstruction.
ArnaudBelcour
commented
8 months ago
Some XML files created by Pathway Tools (and taken by m2m when using the
--pwt-xmloption) have incorrect IDs for SBML format . Indeed some metabolite IDs can begin with a number which is forbidden in SBML format leading to error when these files are read bypython-libsbml, for example when creating the target files from the addedvalue.A fix is to rename all of these IDs by prefixing them with
M_just after the reconstruction.