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pydab's Introduction

pydab

A blazingly fast Python package for modifying and converting DAB files

Installation

pip install pydab

Alternatively, install the latest dev version from github

pip install git+https://github.com/krishnanlab/pydab

Quick start

Convert a DAB file to a DAT file, i.e., tab separated edgelist file with three columns.

Gene1 Gene2 Weight12
Gene1 Gene3 Weight13
...

To convert a DAB file data.dab into data.dat, simply run

pydab -i data.dab -o data.dat

Some up-coming features

  • DAT -> DAB
  • Export to .npz dense array
  • Export to .npz CSR (directly supported by PecanPy)
  • More

pydab's People

Contributors

remylau avatar dependabot[bot] avatar pre-commit-ci[bot] avatar

Stargazers

Tim O'Guin avatar Hao Yuan avatar avatar

Watchers

Arjun Krishnan avatar avatar

pydab's Issues

Save as csr numpy array `.csr.npz`

  • Directly supported by PecanPy
  • Make compatible with scipy.csr, which has the following fields
    • indices (same as in pecanpy csr, but int32, instead of uint32)
    • indptr (same as in pecanpy csr, but in int32, instead of uint32)
    • data (same as in pecanpy csr, but in float64, instead of float32)
    • format -> array(b'csr', dtype='|S3')
    • shape -> n x n, int type

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