3DGenomes / TADbit

TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models

GNU General Public License v3.0

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tadbit model

fixed problem with random seed not being used
reorganize temporary folders to avoid clashing (still work to do)

StructuralModel(s)

Fixes

consistency and accessibility were not returning values when plotting was skipped
New function
- to compute model volume (gross approximation)
- to change the coordinates of particles with no restraints, and place them in a straight line between the two closest particles with restraints.

performance

when reading hic data: faster iteration over matrix fragments

scripts

added script to convert tadbit map files to HiCUP-like bam files

This change is