README.md

Pyccs

Detecting cyclic consensus sequences in nanopore long reads

pip install pyccs

Usage

>>> from pyccs import find_consensus
>>>
>>> segment = "TCCCGGTCATCATAACCCCGATCGTACCCTCTGTCATAATAGTCTCGGCGGCGAGAACTGCCACTGTAAATCTGATCCCTGTCTTGAGCTGCTCTCCATCCACCTCCCTCCACCACCTCCTCCTCTGTATGATCTGCTGTAATAG"
>>>
>>> segment_str, ccs_seq = find_consensus(segment * 3)
>>> segment_str
'10-155;155-300;300-434'
>>>
>>> ccs_seq
'CATAACCCCGATCGTACCCTCTGTCATAATAGTCTCGGCGGCGAGAACTGCCACTGTAAATCTGATCCCTGTCTTGAGCTGCTCTCCATCCACCTCCCTCCACCACCTCCTCCTCTGTATGATCTGCTGTAATAGTCCCGGTCAT'
>>>
>>> len(segment), len(ccs_seq)
(145, 145)

License

The code is released under the MIT License. See the LICENSE file for more detail