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My one-stop-shop for bioinformatics utilities that I have written over the years.
- Free software: MIT license
## Clone the repo git clone [email protected]:gouinK/kgbio.git ## Navigate to repo cd kgbio ## To install just utils and helpers pip install . ## To install seq module pip install .[seq] ## To install scseq module pip install .[scseq] ## To install everything pip install .[seq,scseq]
The utils module contains plotting helper functions.
The seq module contains functions related to fastq processing.
The scseq module contains functions related to single-cell-sequencing processing.
- utils
- -> plotting.py
- seq
-> rawdata.py
-> post_aln.py
- scseq
-> generalfunctions.py
-> qcfunctions.py
-> dgexfunctions.py
-> populationfunctions.py (work in progress, no guarantees)
-> airrfunctions.py (work in progress, no guarantees)
Not currently active: https://kgbio.readthedocs.io/
Not currently implemented:
To run all the tests run:
tox
Note, to combine the coverage data from all the tox environments run:
| Windows | set PYTEST_ADDOPTS=--cov-append tox |
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| Other | PYTEST_ADDOPTS=--cov-append tox |