plot_denovo_motifs

plot_denovo_motifs.py

from clipper.src import CLIP_analysis
import os

viz = CLIP_analysis_display.ClipVisualization()

def plot_denovo_motifs(bedtool, fig=None):
    root = "/Users/gpratt/bioinformatics/yeolab/iPython_Notebook/fox2/"
    out_dir = os.path.join(root, "assigned/")
    fasta_dir = os.path.join(root, "fasta/")
    cluster_name = os.path.basename(bedtool.fn)
    cluster_out = os.path.join(root, bedtool.fn + "_homer")
                               
    cluster_regions = CLIP_analysis.assign_to_regions(tool=bedtool, 
                                                      clusters=cluster_name, 
                                                      regions=regions, 
                                                      assigned_dir = out_dir)

    CLIP_analysis.make_fasta_files_from_regions(cluster_regions, cluster_name, fasta_dir, "/Users/gpratt/bioinformatics/genomes/hg19/chromosomes/all.fa")
    CLIP_analysis.calculate_homer_motifs([5,6,7], regions, cluster_name, fasta_dir, cluster_out)

    if fig is None:
        fig = plt.figure(figsize=(20, 20))
        
    full_grid = gridspec.GridSpec(6, 4)
    motif_grid = gridspec.GridSpecFromSubplotSpec(1, 6,
                                                  subplot_spec=full_grid[4:6, :],
                                                  hspace=0,
                                                  wspace=0)

    viz.build_common_motifs(motif_grid, cluster_out)