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CTCF_orientation

CTCF_orientation is a python tool that produces a pie chart visualizing the CTCF orientation distribution of chromatin loops in a given loop file.

Requirements

  • python 3.7
  • pandas
  • matplotlib

Usage

ctcf_orientation.py -l <loopfile> -m <motiffile> -o <outputfile>

Parameters

  • -l; loop file: Pairedbed file of loops with the format "chromosome1 anchor1_start anchor1_end chromosome2 anchor2_start anchor2_end"
  • -m; motif file: CTCF motif file in the format "chromosome start end name strength orientation pvalue qvalue sequence", although only "chromosome start end" will be used, with the other columns optional.
    • -o; output file: Desired file name for the outputted piechart with extensions available in matplotlib.
  • h; help: Helpful information for usage.

Example

ctcf_orientation.py -l ./test_data/data/grubert_hg19_gm12878_original_loops.bed -m ./test_data/CTCF.bed -o ./test_data/gm12878_hg19_grubert_loops_ctcf_piechart.svg

Thanks

  • CTCF, Source for CTCF motif files and ideas.
  • CTCF_orientation, source of core program and root of all code