comparison COBRAxy/utils/general_utils.py @ 394:a0b53ccc73a8 draft

Uploaded

393:52658ddcaa5d

import zipfile
import gzip
import bz2
from io import StringIO

class ValueErr(Exception):
    def __init__(self, param_name, expected, actual):
        super().__init__(f"Invalid value for {param_name}: expected {expected}, got {actual}")

            raise Exception(f"Error during model extraction: {str(e)}")
        


    def __str__(self) -> str: return self.value

394:a0b53ccc73a8

import zipfile
import gzip
import bz2
from io import StringIO



class ValueErr(Exception):
    def __init__(self, param_name, expected, actual):
        super().__init__(f"Invalid value for {param_name}: expected {expected}, got {actual}")

            raise Exception(f"Error during model extraction: {str(e)}")
        


    def __str__(self) -> str: return self.value


def convert_genes(model,annotation):
    from cobra.manipulation import rename_genes
    model2=model.copy()
    try:
        dict_genes={gene.id:gene.notes[annotation]  for gene in model2.genes}
    except:
        print("No annotation in gene dict!")
        return -1
    rename_genes(model2,dict_genes)

    return model2