Metadata-Version: 2.1
Name: repeatfinder
Version: 1.8
Summary: A package for finding repeats in a DNA sequence
Home-page: https://github.com/deprekate/RepeatFinder
Author: Katelyn McNair
Author-email: deprekate@gmail.com
License: UNKNOWN
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >3.5.2
Description-Content-Type: text/markdown
License-File: LICENSE.txt
Requires-Dist: genbank

# RepeatFinder
A python package to quickly find repeats in a DNA sequence


##  Installing
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
```

## Usage
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)
```


