BinaryFileSearch - Query sorted files in a RAM-efficient way!

Binary search algorithm for big sorted files that cannot be read into RAM.

Requirements:

• File must be sorted by the first column.
  • bash, for integers: sort -n --key=1,1 --field-separator=$'\t' --output=file.txt.sorted file.txt
  • bash, for text: LC_ALL=C sort --key=1,1 --field-separator=$'\t' --output=file.txt.sorted file.txt
• Every line must begin with the sorted string/integer, followed by a separator.
• There may be multiple lines beginning with the same string/integer. (the script will return a list of lines that start with the same string/integer)

Installation:

pip install binary_file_search

Usage:

from binary_file_search.BinaryFileSearch import BinaryFileSearch
with BinaryFileSearch('/path/to/file', sep="\t", string_mode=True) as bfs:
    # assert bfs.is_file_sorted()  # test if the file is sorted.
    lines = bfs.search('query')  # get lines that begin with 'query'

Parameters

Results

The function returns a list of lines, the lines being separated by paramter sep. Example:

[
    ['query', 'l1_col2', 'l1_col3', ...],  # first line that starts with 'query'
    ['query', 'l2_col2', 'l2_col3', ...],  # second line that starts with 'query'
    ...
]

If the query cannot be found, a KeyError is raised.

Credit:

Inspired by https://www.geeksforgeeks.org/python-program-for-binary-search/

Licence:

MIT License

Copyright (c) 2020 Thomas Roder

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.