A python package to quickly find repeats in a DNA sequence
To get, you can either install via pip with the command:
pip install repeatfinder
or you can fetch the source, compile, theninstall the module:
git clone https://github.com/deprekate/RepeatFinder
cd RepeatFinder
python3 setup.py install
Import and use the module as normal
import repeatfinder as rf
my_reps = rf.get_repeats('GGGGGGGGGGGGcAAAAAAAAAAAAgctacgatggagctgacGGGGGGGGGGGGtAAAAAAAAAAAAt')
You can even allow for gaps in the repeats by using the keyword gap
my_reps = rf.get_repeats('GGGGGGGGGGGGcAAAAAAAAAAAAgctacgatggagctgacGGGGGGGGGGGGtAAAAAAAAAAAAt', gap = 1)
The return values are an iterable list containing four-tuples, where the first and second tuple correspond to the coordinates of one of the repeat pairs, and the third and fourth correspond to the other repeat. The list is sorted with the higher scoring repeat pairs coming first.
To run the example script:
python3 test.py
and the output would be the following
non gapped repeats
(1, 12, 43, 54)
(1, 11, 44, 54)
(2, 12, 43, 53)
(14, 25, 56, 67)
(14, 24, 57, 67)
(15, 25, 56, 66)
gapped repeats
(1, 25, 43, 67)
(1, 11, 44, 54)
(2, 12, 43, 53)
(14, 24, 57, 67)
(15, 25, 56, 66)