from basepair.imports import *

Using TensorFlow backend.

2018-12-11 19:45:44,010 [WARNING] git-lfs not installed

nexus_mr = ModiscoResult("nexus_deeplift_modisco.h5")
nexus_mr.open()

nexus_patterns = [nexus_mr.get_pattern(pattern_name) for pattern_name in nexus_mr.patterns()]

len(nexus_patterns)

122

modisco_dir = "/users/amr1/bpnet/basepair/src/pipeline_chipseq/modisco/"
mr = ModiscoResult(modisco_dir+"modisco.h5")
mr.open()

chipseq_patterns = [mr.get_pattern(pattern_name) for pattern_name in mr.patterns()]

len(chipseq_patterns)

8

from modisco.visualization import viz_sequence
import matplotlib.pyplot as plt
%matplotlib inline

for cs_pattern in chipseq_patterns:
    
    sim_scores = np.array([cs_pattern.similarity(nx_pattern) for nx_pattern in nexus_patterns])
    best_score = np.max(sim_scores)
    best_match_id = np.argmax(sim_scores)
    
    print("ChIPseq Pattern: ")
    viz_sequence.plot_weights(cs_pattern.seq, figsize=(20,3))
    
    print("Best ChIP-Nexus Match: ")
    viz_sequence.plot_weights(nexus_patterns[best_match_id].seq, figsize=(20,3))
    
    print("\n\n\n\n")

ChIPseq Pattern: 

Best ChIP-Nexus Match: 

ChIPseq Pattern: 

Best ChIP-Nexus Match: 

ChIPseq Pattern: 

Best ChIP-Nexus Match: 

ChIPseq Pattern: 

Best ChIP-Nexus Match: 

ChIPseq Pattern: 

Best ChIP-Nexus Match: 

ChIPseq Pattern: 

Best ChIP-Nexus Match: 

ChIPseq Pattern: 

Best ChIP-Nexus Match: 

ChIPseq Pattern: 

Best ChIP-Nexus Match: