Main improvements in the past releases:
First release of pypath, for initial testing.
Lots of small improvements in almost every module
Networks can be read from local files, remote files, lists or provided by any function
Almost all redistributed data have been removed, every source downloaded from the original provider.
First version with partial Python 3 support.
pyreact module with BioPaxReader and PyReact classes added
Process description databases, BioPax and PathwayCommons SIF conversion rules are supported
Format definitions for 6 process description databases included.
Many classes have been added to the plot module
All figures and tables in the manuscript can be generated automatically
This is supported by a new module, analysis, which implements a generic workflow in its Workflow class.
homology module: finds the homologs of proteins using the NCBI Homologene database and the homologs of PTM sites using UniProt sequences and PhosphoSitePlus homology table
ptm module: fully integrated way of processing enzyme-substrate interactions from many databases and their translation by homology to other species
export module: creates
pandas.DataFrameor exports the network into tabular file
TF Regulons database included and provides much more comprehensive transcriptional regulation resources, including literature curated, in silico predicted, ChIP-Seq and expression pattern based approaches
Many network resources added, including miRNA-mRNA and TF-miRNA interactions
New, more flexible network reader class
Full support for multi-species molecular interaction networks (e.g. pathogene-host)
Better support for not protein only molecular interaction networks (metabolites, drug compounds, RNA)
ChEMBL webservice interface, interface for PubChem and eventually forDrugBank
Silent mode: a way to suppress messages and progress bars