Representative bed file processor

This tool is designed to parse FSLR output files (representative bed files), and create excel files containing separate sheets for various categories of data.

Installation

This is a python tool, available on pypi. To install, run

pip install repbed-processor

Running the tool

Simple examples

To see more information about the available options for running the tool, run:

python -m repbed_processor --help

For a single input file, and using the default probes of interest and default threshold for complex events, simply run:

python -m repbed_processor path/to/your_file.representative.bed

(where 'path/to/your_file.representative.bed' is the path to your FSLR output file)

Other examples

To change the threshold for what you consider to be a complex event, use -c (default is 5):

python -m repbed_processor path/to/your_file.representative.bed -c 10

If you have multiple input files, you may enter them all:

python -m repbed_processor path/to/your_file1.representative.bed path/to/your_file2.representative.bed

And if you would like to analyse multiple input files all together (e.g. combining several controls), use the --mixed-input (or -m) flag:

python -m repbed_processor path/to/your_file1.representative.bed path/to/your_file2.representative.bed --mixed-input

To specify your probes (rather than using the default, 21q1), use the -p option (you must specify -p before each probe):

python -m repbed_processor path/to/your_file.representative.bed -p probe_name -p another_probe

If you would like separate output files for each probe, use the --split (or -s) flag:

python -m repbed_processor path/to/your_file.representative.bed -p probe_name -p another_probe -s

Other options, such as logging and file name customisation, are detailed within the help message (see --help, above)

Issues

Please log issues on GitHub

Licence

MIT (see LICENCE.txt)