kripodb.script¶
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kripodb.script.
main
(argv=['-T', '-E', '-b', 'readthedocs', '-d', '_build/doctrees-readthedocs', '-D', 'language=en', '.', '_build/html'])[source]¶ Main script function.
Calls run method of selected sub commandos.
Parameters: argv (list[str]) – List of command line arguments
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kripodb.script.
make_parser
()[source]¶ Creates a parser with sub commands
Returns: parser with sub commands Return type: argparse.ArgumentParser
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kripodb.script.fragments.
make_fragments_parser
(subparsers)[source]¶ Creates a parser for fragments sub commands
Parameters: subparsers (argparse.ArgumentParser) – Parser to which to add sub commands to
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kripodb.script.fingerprints.
make_fingerprints_parser
(subparsers)[source]¶ Creates a parser for fingerprints sub commands
Parameters: subparsers (argparse.ArgumentParser) – Parser to which to add sub commands to
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kripodb.script.similarities.
make_similarities_parser
(subparsers)[source]¶ Creates a parser for similarities sub commands
Parameters: subparsers (argparse.ArgumentParser) – Parser to which to add sub commands to
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kripodb.script.similarities.
read_fpneighpairs_file
(inputfile, ignore_upper_triangle=False)[source]¶ 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)