01_File_Conversion.ipynb

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    "##### `Optional step: Convert Thermo files (*.raw):`\n",
    "\n",
    "ThermoRawFileParser https://github.com/compomics/ThermoRawFileParser\n",
    "\n",
    "- It is necessary to convert profile data to centroid mzml. If your files do not originate from a thermo instrument, please convert them using proteowizard (see https://proteowizard.sourceforge.io/) and add them to the \"data/mzML/\" directory. "
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    "import glob\n",
    "import os\n",
    "input_raw_files = os.path.join(\"data\", \"raw\")\n",
    "output_mzML_files = os.path.join(\"data\", \"mzML\")\n",
    "!thermorawfileparser --input_directory {input_raw_files} --output_directory {output_mzML_files}"
   ]
  }
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