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
1 maintainer
Metadata
1 maintainer
Release files for pyccs 1.1.0
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Built distributions (wheels)
Total release size: 4.4 MB
Release files / pyccs-1.1.0-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl
| Download URL | pyccs-1.1.0-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl |
|---|---|
| Size | 1.1 MB |
| Tags | CPython 3.10 Linux glibc 2.12+ x86-64 Linux glibc 2.5+ x86-64 |
|
SHA-256 checksum How to use checksums |
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twine/4.0.0 PyPy/7.3.7
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Release files / pyccs-1.1.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl
| Download URL | pyccs-1.1.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl |
|---|---|
| Size | 1.1 MB |
| Tags | CPython 3.9 Linux glibc 2.12+ x86-64 Linux glibc 2.5+ x86-64 |
|
SHA-256 checksum How to use checksums |
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twine/4.0.0 PyPy/7.3.7
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Release files / pyccs-1.1.0-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl
| Download URL | pyccs-1.1.0-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl |
|---|---|
| Size | 1.1 MB |
| Tags | CPython 3.8 Linux glibc 2.12+ x86-64 Linux glibc 2.5+ x86-64 |
|
SHA-256 checksum How to use checksums |
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No |
| Uploaded via |
twine/4.0.0 PyPy/7.3.7
|
Release files / pyccs-1.1.0-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl
| Download URL | pyccs-1.1.0-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl |
|---|---|
| Size | 1.1 MB |
| Tags | CPython 3.7 CPython 3.7 pymalloc Linux glibc 2.12+ x86-64 Linux glibc 2.5+ x86-64 |
|
SHA-256 checksum How to use checksums |
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No |
| Uploaded via |
twine/4.0.0 PyPy/7.3.7
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