chipseqpeaks

A wrapper for MACS2 that abstracts out some things and makes it easier to use. Thanks due to Joshua Chiou for inspiration and contributions.

Warning: Before using chipseqpeaks, please make sure that one of the environment variables TMPDIR, TEMP, or TMP is set to an appropriate path. This is the only way to ensure MACS2 writes temporary files to the correct location, and failing to do so may cause errors on some systems. (ง •̀_•́)ง

Installation

pip install chipseqpeaks

or

pip install --user chipseqpeaks

Example API usage

from chipseqpeaks import ChIPSeqPeaks
with ChIPSeqPeaks(<bytes object or path to BAM file>) as cp:
    cp.cleans_up = False
    cp.remove_blacklisted_peaks(<path/to/blacklist.bed>)
    cp.write(<output prefix>)

Example command line usage

For help text, see:

chipseqpeaks-call -h

For ChIP-seq:

chipseqpeaks-call --control input.bam chip.bam

For ATAC-seq:

chipseqpeaks-call --atac-seq atac.bam