compressbinarytable 0.1.7

Compression of binary table

CompressBinaryTable

Basic Usage:

cbt -i input_file -o output_file -c 

Options:

-i = input, required 
-o = output, required 
-c = compression 
-d = decompression 
-t = output type, either csv or tsv 
--override = to override output file if it exist 

Available Python functions:

# Returns numpy array of file as uncompressed, useful for ML (same as load as pandas df, and to_numpy())
cbt_to_array(compressed_file)

# Returns numpy array of name of the mutations as uncompressed, useful for ML, (same as load pandas df and use df.colums)
cbt_columns(compressed_file)

Required file example:

CSV:

strain_name,mut1,mut2,mut3,mut4,outcome strain1,0,1,1,1,1,1 strain2,0,0,1,1,1,0 strain3,0,1,0,1,1,0 strain4,1,1,1,1,1,1

TSV:

strain_name mut1 mut2 mut3 mut4 outcome strain1 0 1 1 1 1 1 strain2 0 0 1 1 1 0 strain3 0 1 0 1 1 0 strain4 1 1 1 1 1 1

CBT:

1;mut1;mut2;mut3;mut4;outcome strain1;6;43;87;102 strain2;16;43;87;102 strain3;6;53;78;112 strain4;61;413;824;942