General-use scripts

File Processing, handling HPC runs, etc

cleanHiM_run.py

Cleans the directories and log files created by pyHiM in previous runs.

Usage: clean_him_run [-F ROOTFOLDER] [-P PARAMETERS] [-A ALL]

optional arguments:
  -F ROOTFOLDER, --rootFolder ROOTFOLDER
                        Folder where the analysis has been performed
  -P PARAMETERS, --fileParameters PARAMETERS
                        Parameters file. Default: parameters.json
  -A ALL, --all ALL
                        Delete all folders and all created files

lndir.py

Creates link for files in a second directory (useful to analyze data in a new folder without copying raw data files).

Usage: lndir "/user_home/Repositories/pyHiM/*py" ~/Downloads/test

Use quotation marks in the first argument if using wildcards.

zipHiM_run.py

Zip all output files from a pyHiM run. It excludes .npy and .tif files. Useful to retrieve results from a run from an HPC cluster.

Usage: zip_him_run [-F ROOTFOLDER] [-P PARAMETERS] [-R RECURSIVE]

optional arguments:
  -F ROOTFOLDER, --rootFolder ROOTFOLDER
                        Folder where the analysis has been performed
  -P PARAMETERS, --fileParameters PARAMETERS
                        Parameters file. Default: parameters.json
  -R RECURSIVE, --recursive RECURSIVE
                        Zip files inside folders of current directory

unzipHiM_run.py

Unzips HiM_run.tar.gz recursively. Useful to unzip the results from several folders retrieved from a run in an HPC cluster.

Usage: unzip_him_run [-F ROOTFOLDER] [-R RECURSIVE]

optional arguments:
  -F ROOTFOLDER, --rootFolder ROOTFOLDER
                        Folder where the HiM_run.tar.gz is located
  -R RECURSIVE, --recursive RECURSIVE
                        Unzip files inside folders of current directory

Post-processing scripts

npy_to_tiff

This script will convert Numpy array files into imageJ-readable TIFs. Images will be rescaled to (0, 2^14) range and will be histogram normalized using skimage.exposure.equalize_adapthist().

You can invoke this in two ways:

• Use find and send the list of files as arguments:

npy_to_tiff $(find -name "*ch0*_2d_registered.npy")

• Otherwise you can pipe the results as follows:

ls *ch0*_2d_registered.npy | npy_to_tiff