ftir-renamer 0.5

File renamer for FTIR files

FTIR File Renamer

Introduction

Renames files from the FTIR based on strict naming scheme

Installation

From the command line in the folder in which you would like to install the program:

pip install ftir_renamer

Upgrade

pip install --upgrade ftir_renamer

Requirements

• Unix-like environment
• Spreadsheet of FTIR-related metadata (with .XLSX extension)
• The .spc output files corresponding to the FTIR IDs in the spreadsheet

ftir_rename

Shell script automating the renaming of files from a USB stick

Required Argument

-f
The absolute path to the folder containing the .spc files

Running

Example command to run the script

ftir_rename -f /path/to/FTIR_files

renamer.py

Python script that renames .spc files

Required Arguments

-s
The path of the folder containing the FTIR output files
-f 
Absolute path to the spreadsheet containing the FTIR metadata
-o
The absolute path of the folder to store the renamed files

Running

Example command to run the script

renamer.py -f /path/to/FTIR.xlsx -s /path/to/files -o /path/to/outputs

Usage

usage: renamer.py [-h] -s SEQUENCEPATH -f FILENAME -o OUTPUTPATH

Rename files for FTIR experiments using strict naming scheme

  -h, --help            show this help message and exit
required arguments:
  -s SEQUENCEPATH, --sequencepath SEQUENCEPATH
                        Path of .spc files to process.
  -f FILENAME, --filename FILENAME
                        Name of .xls(x) file with renaming information. Must
                        conform to agreed upon format. This file must be in the
                        supplied sequencepath.
  -o OUTPUTPATH, --outputpath OUTPUTPATH
                        Optionally specify the folder in which the renamed
                        files are to be stored. Provide the full path e.g.
                        /path/to/output/files