PYTHON:
- cython:
pip3 install cython
TOOLS:
- bedtools: https://bedtools.readthedocs.io/en/latest/ version >= 2.26.0
git clone https://github.com/ubercomrade/pipeline.git
cd pipeline/
pip3 install -e .
The command pmwComparator.py -h return:
usage: pwmComparator.py [-h] [-nnames N [N ...]] [-f FPR] [-C CPU_COUNT]
bed N genome output N [N ...]
positional arguments:
bed path to BED file
N promoters of organism (hg38, mm10)
genome path to genome fasta file
output output dir
N list of path to PFMs to use (./model1.pfm,
./model2.pfm ...)
optional arguments:
-h, --help show this help message and exit
-names N [N ...] list of names for models (name1, name2 ...)
-f FPR, --FPR FPR FPR, def=1.9*10^(-4)
Example run:
pwmComparator.py \
path/to/peaks.bed \
hg38 \
/path/to/genomes/hg38.fa \
./output_dir \
./model1.pfm \
./model2.pfm \
./model3.pfm \
Copyright (c) 2020 Anton Tsukanov
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The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
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