Pyna colada is a python module and application using 'straw' and 'juice-tools' to provide a more useful API to work with .hic Hi-C experiments files.
Developed by Costas Bouyioukos at Universite Paris Cite and UMR7216 Paris Epigenetics since Dec. 2019
Pyna colada includes a library (pyna_colada) providing easy access and visualisation to .hic files on top of the hic-straw library and an executable script (pyna-collda) that visualises contacts between any gene (or regions) list of interest by simply using an ENSEMBL (or other) annotation file.
Just run the setup.py script to install the module and the executable in your path of interest. Typically:
python setup.py install --user
A typical run of pyna-collada can be performed by specifying two input files as positional arguments and an output .html file with the interactive plotly visualisation:
pyna-collada <.hic_input_file> <annotation_file> <output_html_file> [options]
Where:
- <hic_input_file>: is a binary .hic file usually the outcome of HiC experiment.
- <annotation_file>: is a table (tab delimited) file where each line represents a gen (or region) of interest and with 3 (at least) mandatory columns "Gene_ID" (any unique identifier), "Gene_start", "Gene_end" (the beginning and end of gene in genomic coordinates), "Chromosome" (the chromosome where the gene resides), "Strand" (the + or - strand), "Gene_name" (the common gene name for visualisation purposes)
- <output_html_file>: the path/name of the output file.
A description of the available options (and their default values) is fully accessible by the --help or -h command line flags.
- pandas
- hic-straw
- numpy
- plotly
Developer/maintainer Costas Bouyioukos https://github.com/cbouyio, any comments or question please drop a line at: costas.bouyioukos@u-paris.fr