prodmx 0.1.0

Protein Functional Domain Analysis based on Compressed Sparse Matrix

## ProdMX : Protein Functional Domain based on Compressed Sparse Matrices

ProdMX is a tool with user-friendly utilities developed to facilitate high-throughput analysis of protein functional domains and domain architectures. The ProdMX employs a compressed sparse matrix algorithm to reduce computational resources and time used to perform the matrix manipulation during functional domain analysis.

### Dependencies

• Python 3.5 or newer and the following packages:

  • [pandas](https://github.com/pandas-dev/pandas)

  • [h5py](https://github.com/h5py/h5py)

  • [numpy](https://github.com/numpy/numpy)

  • [tqdm](https://github.com/tqdm/tqdm)

  • [scipy](https://github.com/scipy/scipy)

### Installation from source

` git clone https://github.com/visanuwan/prodmx python -m pip install prodmx ` ### Usage

Generally, the use of the ProdMX tool starts with constructing the compressed sparse matrix of either protein functional domains or domain architectures in a command-line environment. The input of ProdMX is a tab-delimited file containing two columns of genome labels and the path to their HMMER results.

Protein functional domain

` prodmx-buildDomain [-h] [-v] [-i INPUT] [-o OUTPUT] [-k] `

Domain architecture

` prodmx-buildArchitecture [-h] [-v] [-i INPUT] [-o OUTPUT] [-k] ` For the detail of commands and examples, see the example of analyses using ProdMX in [Jupyter Notebook.](test/prodmx_example.ipynb)