Prerequisites

Mac

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/"

Linux

sudo apt-get install openssl
sudo apt-get install default-libmysqlclient-dev # on vm image with docker

Install the module using:

sudo python setup.py install
# or 
python setup.py install --user

Module on the production:

test the module:

./getbw

import _bw
_bw.getrp('your_bigWig', 'annotation_TSS', 'output', 10000.0)

Command line

regpot.py -n out -b test/42359_treat.bw --tss test/test_tss.bed

adjust -a ALPHA for decay rate.

Further instruction

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       -

parameter to delete one specific region

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)