transfer_convert

A collection of scripts for automating conversion to Photon-HDF5, archival and analysis of smFRET measurements using multiprocessing (each file is processed in a different CPU).

A brief description of each script follows.

batch_convert.py

Convert all files in a specified folder in batch. If the --monitor argument is passed, monitors a given folder. When a new YAML file appears in the same folder with the same name as a data file, it starts these processing steps:

copy the data to a temp folder
convert data to Photon-HDF5 using the metadata from the YAML file
copy all files to and archival folder
optionally run smFRET analysis

Data files can be processed in parallel.

Type ./batch_convert.py -h for more info on how to use the script.

batch_analyze.py

Analyze all the Photon-HDF5 files in a given folder using a default notebook or any other specified notebook. Multiple files can be processed in parallel. For optimal performances it is suggested to do not exceed the number of CPUs.

Type ./batch_analysis.py -h for more info on how to use the script.

analize.py

Analyze a single Photon-HDF5 file using a the specified notebook.

Type ./analyze.py -h for more info on how to use the script.

transfer.py

Module used for processing a single file (copy, conversion, analysis). The script monitor.py build a multiprocessing pool and calls functions defined in transfer.py to process several files in parallel.

Installation

Download the repository and run the scripts directly from the repo folder (no installation).

Dependencies

python 3.6 (older versions may work)
jupyter notebook 5+
jupyter nbconvert 5+
pyyaml
tqdm (progress bar)
FRETBursts 0.6.3+
phconvert 0.7.3+
niconverter

See also conda_environment_linux.yml.

How to cite

If you use this code for a publication, please cite as:

48-spot single-molecule FRET setup with periodic acceptor excitation
A. Ingargiola, M. Segal, A. Gulinatti, I. Rech, I. Labanca, P. Maccagnani, M. Ghioni, S. Weiss, X. Michalet
bioRxiv 156182; 2017. doi: https://doi.org/10.1101/156182

Copyright (C) 2017 The Regents of the University of California, Antonino Ingargiola and contributors.

This work was supported by NIH grants R01 GM069709 and R01 GM095904.

License

multispot-software/transfer_convert

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