brew install openssl
export C_INCLUDE_PATH=${C_INCLUDE_PATH}:/usr/local/Cellar/openssl/your_version/include
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/Cellar/openssl/your_version/lib/"
sudo apt-get install openssl
sudo apt-get install default-libmysqlclient-dev # on vm image with docker
sudo python setup.py install
# or
python setup.py install --user
./getbw
import _bw
_bw.getrp('your_bigWig', 'annotation_TSS', 'output', 10000.0)
regpot.py -n out -b test/42359_treat.bw --tss test/test_tss.bed
adjust -a ALPHA
for decay rate.
annotation_TSS --tss
should be formatted as:
chr1 11873 11874 NR_046018:DDX11L1 0 +
chr1 17436 17437 NR_107063:MIR6859-3 0 -
chr1 17436 17437 NR_128720:MIR6859-4 0 -
output demo -n
, 5th
column is the regulatory potential score from bigWig:
chr1 11873 11874 NR_046018 208.234170501 DDX11L1 +
chr1 17436 17437 NR_107063 219.513716641 MIR6859-3 -
chr1 17436 17437 NR_128720 219.513716641 MIR6859-4 -
This removal of region does not consider strand, e.g., to delete all promoter +/- 1kb:
_bw.getrp('test/test.bw', 'test/test_tss.bed', 'test/out.tab', 10000.0, -1000, 1000)
Below would delete the downstream 1kb in the gene body for positive strand transcript, but upstream 1kb for negative strand transcript.
_bw.getrp('test/test.bw', 'test/test_tss.bed', 'test/out.tab', 10000.0, 0, 1000)