Пайплайн написан в рамках GenHack 2020 для решения задачи - Предсказание полимеразной активности новых Φ29 ДНК-полимераз.
PYTHON:
- python >= 3.7
- biopython:
pip3 install biopython
TOOLS:
- HMMER: conda install -c conda-forge hammer or from source http://hmmer.org
git clone https://github.com/ubercomrade/GenHack.git
cd GenHack/
pip install -e .
The command findTarget -h return:
usage: findTarget.py [-h] [-t TMP_DIR] genebank fasta results tag
positional arguments:
genebank path to GeneBank file
fasta path to write Fasta (parsed CDS from GeneBank file)
results dir to write results
tag tag for output files
optional arguments:
-h, --help show this help message and exit
-t TMP_DIR, --tmp TMP_DIR
tmp dir
findTarget.py \
path/to/gbk/12_45.gbk \
path/to/write/parsed/CDS/12_45.fasta \
dir/to/write/res/ \
tag-of-files
Copyright (c) 2020 Trituration
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