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        "description": "FTIR File Renamer\n==============\n### Introduction\n\nRenames files from the FTIR based on strict naming scheme\n\n### Virtual Environment\n\nActivate your FTIR renamer virtual environment\n\n`source ftir_rename/bin/activate`\n\nIf that does not work, your environment may not exist. Create it as follows:\n\n```\npython3 -m venv ftir_rename\nsource ftir_rename/bin/activate\n```\n\n### Installation\n\nFrom the command line in the folder in which you would like to install the program:\n\n`pip install ftir_renamer`\n\n### Upgrade\n\n`pip install --upgrade ftir_renamer`\n\n### Requirements\n- Unix-like environment\n- Spreadsheet of FTIR-related metadata (with .XLSX extension)\n- The .spc output files corresponding to the FTIR IDs in the spreadsheet\n\n\n## ftir_rename\n\nShell script automating the renaming of files from a USB stick\n\n### Required Argument\n\n```\n-f\nThe absolute path to the folder containing the .spc files. Note that either this folder or its parent must contain an Excel file named FTIR.XLSX \nthat contains all the required metadata for renaming.\n\n```\n\n### Optional Argument\n\n```\n-c\nUse the \"classic method of renaming the files: \nOriginal File Name: FTIR0182-1_2017-05-26T11-13-47.spc\nNew File Name: GN_Klebsiella_BHI_AN_CFIA_FTIR0182_C2_2017_May_26_CA01_OLC0027_2017-05-26T11-13-47.spc\n```\n\n### Running\n\n##### Example command to run the script\n\n`ftir_rename -f /path/to/FTIR_files`\n\n## renamer.py\n\nPython script that renames .spc files\n\n### Required Arguments\n\n```\n-s\nThe path of the folder containing the FTIR output files\n-f \nAbsolute path to the spreadsheet containing the FTIR metadata\n-o\nThe absolute path of the folder to store the renamed files\n```\n\n### Running \n\n##### Example command to run the script\n\n`renamer.py -f /path/to/FTIR.xlsx -s /path/to/files -o /path/to/outputs`\n    \n##### Usage\n\n```\nusage: renamer.py [-h] -s SPECTRA_PATH -f FILENAME -o OUTPUTPATH\n\nRename files for FTIR experiments using strict naming scheme\n\n  -h, --help            show this help message and exit\nrequired arguments:\n  -s SPECTRA_PATH, --sequencepath SPECTRA_PATH\n                        Path of .spc files to process.\n  -f FILENAME, --filename FILENAME\n                        Name of .xls(x) file with renaming information. Must\n                        conform to agreed upon format. This file must be in the\n                        supplied sequencepath.\n  -o OUTPUTPATH, --outputpath OUTPUTPATH\n                        Optionally specify the folder in which the renamed\n                        files are to be stored. Provide the full path e.g.\n                        /path/to/output/files\n```",
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