A collection of scripts for retrieving Genomics coverage and downstream analysis, this project is based on HDF5 to improve performance when working on large numbers of bigwig genomic tracks.
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dumpHDF5.py
Compute per base coverage from a 1-based bedgraph format file, then dump into the specified hdf5 file
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loadHDF5.py
Load coverage in the regions provided, output the average coverage per base, heatmap and composite plot. All regions must have the same length
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loadHDF5_mpi.py
MPI version of loadHDF5.py
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loadHDF5_pearson.py
Load genome-wide coverage or coverage in the regions if provided region file, concatenate them and chop into bins, compute pearson/spearman correlation of these bins, output correlation matrix, heatmap.
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loadHDF5_pearson_mpi.py
MPI version of loadHDF5_pearson_mpi.py