Hello I am new to python and Cobra, i would be grateful if you can provide me with steps to open an XML file from the computer and/or from online database, i tried the commands on Cobra documentation but i can't apply it.

[Rahmaabubakr]

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• I looked through similar issues on GitHub.
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Question

[cdiener]

Can you describe what code you ran exactly and what errors you are getting?

[Rahmaabubakr]

I m applying from this file step by step, starting from this steps, i can apply it.

from pathlib import Path
from cobra.io import load_json_model, save_json_model, load_matlab_model, save_matlab_model, read_sbml_model, write_sbml_model
import logging

data_dir = Path(".") / ".." / "src" / "cobra" / "data"
data_dir = data_dir.resolve()

print("mini test files: ")
print(", ".join(str(i) for i in data_dir.glob('mini*.*')))

textbook_model = load_model("textbook")
ecoli_model = load_model("iJO1366") 
logging.getLogger("cobra.io.sbml").setLevel(logging.ERROR)salmonella_model = load_model("salmonella")

[Rahmaabubakr]

Thank you

[Rahmaabubakr]

and these are the errors

OSError                                   Traceback (most recent call last)
[/home/rahma/RA/habolla.ipynb](https://file+.vscode-resource.vscode-cdn.net/home/rahma/RA/habolla.ipynb) Cell 52 line 2
      [1](vscode-notebook-cell:/home/rahma/RA/habolla.ipynb#Y131sZmlsZQ%3D%3D?line=0) mini_fbc2_path = data_dir [/](https://file+.vscode-resource.vscode-cdn.net/) "mini_fbc2.xml"
----> [2](vscode-notebook-cell:/home/rahma/RA/habolla.ipynb#Y131sZmlsZQ%3D%3D?line=1) read_sbml_model(str(mini_fbc2_path.resolve()))

File [~/RA/lib/python3.10/site-packages/cobra/io/sbml.py:460](https://file+.vscode-resource.vscode-cdn.net/home/rahma/RA/~/RA/lib/python3.10/site-packages/cobra/io/sbml.py:460), in read_sbml_model(filename, number, f_replace, **kwargs)
    458     return _sbml_to_model(doc, number=number, f_replace=f_replace, **kwargs)
    459 except IOError as e:
--> 460     raise e
    462 except Exception as original_error:
    463     cobra_error = CobraSBMLError(
    464         "Something went wrong reading the SBML model. Most likely the SBML"
    465         " model is not valid. Please check that your model is valid using "
   (...)
    470         "at https://github.com/opencobra/cobrapy/issues ."
    471     )

File [~/RA/lib/python3.10/site-packages/cobra/io/sbml.py:457](https://file+.vscode-resource.vscode-cdn.net/home/rahma/RA/~/RA/lib/python3.10/site-packages/cobra/io/sbml.py:457), in read_sbml_model(filename, number, f_replace, **kwargs)
    402 """Read SBML model from given filename.
    403 
    404 If the given filename ends with the suffix ''.gz'' (for example,
   (...)
    454 File handles to compressed files are not supported yet.
    455 """
...
    510     # file handle
    511     doc: libsbml.SBMLDocument = libsbml.readSBMLFromString(filename.read())

OSError: The file with '/home/rahma/src/cobra/data/mini_fbc2.xml' does not exist, or is not an SBML string. Provide the path to an existing SBML file or a valid SBML string representation:
Output is truncated. View as a [scrollable element](command:cellOutput.enableScrolling?d83964c3-d25e-43f4-a55e-11e96513ab35) or open in a [text editor](command:workbench.action.openLargeOutput?d83964c3-d25e-43f4-a55e-11e96513ab35). Adjust cell output [settings](command:workbench.action.openSettings?%5B%22%40tag%3AnotebookOutputLayout%22%5D)...

[cdiener]

Perfect, thanks for providing that information. The documentation is a bit confusing there, apologies for that. The first part of the code uses the GitHub repo structure to show all the included test files but this won't work on a normal installation, so those files won't be in the expected location and causes the errors you are seeing.

For a minimal example, the following will be enough:

from cobra.io import load_model

textbook_model = load_model("textbook")
ecoli_model = load_model("iJO1366")

This will load two of the models you can play around with. load_model can also be used to directly open models from reference databases such as BIGG or Biomodels.

The other read_* and load_ functions are there to read model files in various different formats. The most common one is SBML. So for instance if you would download iCHOv1.xml from this site to your home directory, you could read and use it with:

from cobra.io import read_sbml_model

hamster = read_sbml_model("iCHOv1.xml")
print(hamster.summary())

[Rahmaabubakr]

Thank you very much, all your replies and efforts are really appreciated.
I opened the file directly from the repository using load_model, thank you.

Are there any online courses, tutorials or materials that can help me with COBRApy and flux balance analysis?