annadca 0.1.0

Annotation Assisted Direct Coupling Analysis

ANNotation Assisted Direct Coupling Analisis (annaDCA)

This package contains the methods and scripts to train and sample an RBM model provided with data annotations.

Installation

Option 1: from PyPl

python -m pip install annaDCA

Option 2: cloning the repository

git clone https://github.com/rossetl/annaDCA.git
cd annaDCA
python -m pip install .

Usage

After installation, all the main routines can be launched through the command-line interface using the command annadca. To see all the training options do

annadca train -h

To train the model with default arguments do

annadca train -d <path_data> -a <path_annotations> -o <output_directory> -l <model_tag>

Input data format

The input data should be:

• binary variables: plain text format. Each row is one data sample, variables are separated by white spaces
• categorical variables: fasta format. Each data poin is a sequence of tokens with an header on top. The header row starts with >.

Annotation data format

Annotations bust be provided in a csv file with two columns. One column is called (mandatory!) Name, an the other column represents the labels and can have any chosen name.

For categorical varables, the Name field must match one of the headers in the fasta file, while for binay variables the order of the rows is used.

Un-annotated data should not be present in the annotation file.