- Create the first stable Pergola release
- Eliminate files not used
- Modify tag for pergola ontology file. Now is genome_file:term, for pergola: Pergola paper
- Modify the name of pergola_rules by pergola_convert
- Create a -genome option allowing to choose the user whether to generate the genome files or not
- Borrar archivos temporales
- Make write chromosome an option (generate genome file)
- Window and window mean only reachable when bedgraph option is set, control for this. should only be reachable?
- Move jaaba files to examples folder or similar
- Modify tracks create_pybedtools documentation it has the docs of a different class
- Create first release github
- make the package available by pypi
- add dependencies for pypi installation
- Upload C.elegans files
- Clean all code annotations
- Add jaaba_to_pergola to test_all.py
- loadmat function makes library scipy a dependency of the whole package by importing parsers, separate in a different
- Converting jaaba features folder to csv or pergola objects
- Add to unitest the test of the scripts
- Adding pergola_rules to test, for this transform scripts into console_scripts
- Checkings of the code using travis or similar tools
- Create a script for jaaba wrapping all jaaba options
- Implement mean of bedgraph window
- Use file format conventions of bed and gff files (0, 1 etc)
- Read files from ctrax
- Filter by data type
- bedGraph window by default should by 1 or otherwise give an option just to transform bed to bedgraph without window
- Add to test the checking of the creation of bedGraph files with and without binning.
- Create pergola ontology and add it to the website documentation