Fix for pipelines

This allows for absolute paths in running with -out and also lets setup more properly install in local bins.

Small refactoring so it can work in web apps more easily

Basically just made a main() function and streamlined it a bit for command line or webapp.

Fix for windows user install, and optional path to database `-d`

Added -d so users can easily run with a database folder location of their choosing, and removed readline and ncurses so Windows conda install works.

Major changes for user installation, KB location

Also includes fixes to scripts for manuscript as per reviewer questions and comments.

Can now specify folder for phen2gene.py and lib scripts (e.g., /usr/bin or $HOME/bin, etc.) and local for KB (somewhere dedicated for data storage, if desired) thanks to @abolia for the suggestion.

Release of Phen2Gene for Biorxiv

This contains fixes to H2GKB that came from bug fixes to Phenolyzer.

In addition, we have added the whole pipeline for generating the benchmark figure from the paper and all of the benchmark data.

We have added a reproducible Anaconda YML file for running Phen2Gene in Python 3.8.

Updated formatting, first release of HPO2GeneKB

Added JSON formatting, made changes to weights, and added the HPO2Gene-KB. This release contains the initial release of the H2GKB for download, and so is now version 1.0. It is a tarball containing ~14,258 files, one tab-separated value list of genes ranked for each HPO term.

Added benchmark sets data.

adding information content weighting, and HPO term replacement

-Added a new weighting method based on Sanchez's ontology-based information content model.
-Added a pre-compiled outdated HPO terms, some of which are replaced by currently in-use HPO terms. When running Phen2Gene, outdated HPO terms will be replaced automatically.

initial release

If users have question, you are welcome to create an issue.