kripodb.script

kripodb.script.main(argv=['-T', '-E', '-b', 'readthedocs', '-d', '_build/doctrees-readthedocs', '-D', 'language=en', '.', '_build/html'])

Main script function.

Calls run method of selected sub commandos.

Parameters:argv (list[str]) – List of command line arguments

kripodb.script.make_parser()

Creates a parser with sub commands

Returns:parser with sub commands Return type:argparse.ArgumentParser

kripodb.script.fragments.make_fragments_parser(subparsers)

Creates a parser for fragments sub commands

Parameters:subparsers (argparse.ArgumentParser) – Parser to which to add sub commands to

kripodb.script.fingerprints.make_fingerprints_parser(subparsers)

Creates a parser for fingerprints sub commands

Parameters:subparsers (argparse.ArgumentParser) – Parser to which to add sub commands to

kripodb.script.similarities.make_similarities_parser(subparsers)

Creates a parser for similarities sub commands

Parameters:subparsers (argparse.ArgumentParser) – Parser to which to add sub commands to

kripodb.script.similarities.read_fpneighpairs_file(inputfile, ignore_upper_triangle=False)

Read fpneigh formatted similarity matrix file.

Parameters:

• inputfile (File) – File object to read
• ignore_upper_triangle (bool) – Ignore upper triangle of input

Yields:

Tuple((Str,Str,Float)) – List of (query fragment identifier, hit fragment identifier, similarity score)

kripodb.script.similarities.simmatrix_export_run(simmatrixfn, outputfile, no_header, frag1, pdb)

Export similarity matrix to tab delimited file

Parameters:

• simmatrixfn (str) – (Compact) hdf5 similarity matrix filename
• outputfile (file) – Tab delimited output file
• no_header (bool) – Output no header
• frag1 (bool) – Only output *frag1
• pdb (str) – Filename with pdb codes inside

kripodb.script.dive.dense_dump_sc(sc)

Dump dense matrix with zeros