# Parameters
sample_name = "LVR;8wks;D;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_202-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_202-naivegw/NaiveauPRC.txt"
homer_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_scans"

from matlas.modisco_report import modisco_report_pipeline, display_metadata
reportfile= "/mnt/lab_data/kundaje/msharmin/mouse_hem/with_tfd/full_mouse50/filtering samples_MS2.xlsx"
sheetname = "filter23"

load data from labcluster

Using TensorFlow backend.
2019-07-23 01:39:30,377 [WARNING] git-lfs not installed

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	Liver (Adult 8 weeks)
Cell Group	Other Tissues
Experiment Name	DHS
Experiment Group	GEO

Pipeline Output

replicate	Naïve overlap peaks	IDR peaks	TSS enrichment (< 8 is very poor <10 is low)	Final number of unique mapping, dup-filtered, chrM filtered reads	Number of reads in called peak regions	Fraction of reads in called peak regions	Number of reads in promoter regions	Fraction of reads in promoter regions	Number of reads in enhancer regions	Fraction of reads in enhancer regions
rep1	183134	138845	7.2165	108721829	34389719	0.3164	10494514	0.0965	46053674	0.4237

Modelling Metadata

Metric	Value
auPRC	0.5037
Calibrated Recall at 50% FDR	0.279
Number of Positive Examples in Test Data	151013
Number of Negative Examples in Test Data	7919838
Imbalance Ratio in Test Data	0.0187
Test Chromosomes	chr2, chr3, chr19

from matlas.modisco_report import display_comparative_motif_sets
display_comparative_motif_sets(sample_name, homer_root, modisco_root)

TF-MoDISco is using the TensorFlow backend.

Number of CISBP motifs obtained by TF-MoDISco and Homer-denovo

Shared Motifs

Motif Name	Modisco	Homer
Nfic
Hnf4g
Ctcf

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Foxi1		absent
Gata2		absent
Sp3		absent
Tcfec		absent
Erf		absent
9430076C15Rik		absent
Nfia		absent
Mbtps2		absent
Bach1		absent
Nr5a2		absent
Foxa1		absent
Smarcc2		absent
Cebpb		absent
Onecut3		absent
Irf1		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Foxa3	absent
Srebf2	absent
Sp2	absent
Nr4a1	absent
Cebpa	absent
Gabpa	absent
Esrrg	absent
Hnf1b	absent
Zfp143	absent

modisco_report_pipeline(sample_name, modisco_root, mitra_subdir, task_dir, database_name, 
                        importance=True, render=True)

rsync -t -av /srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019/task_202-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_202-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_202-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_1, # patterns: 21, # seqlets: 22836, Positive for: LVR;8wks;D;GEO

• pattern_0: # seqlets: 3934

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Hnf4g, Nr1h2, Pparg, Ppard, Nr4a3

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_1: # seqlets: 3213

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Cebpb, Cebpa, Cebpd, Cebpg, Cebpe

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_2: # seqlets: 2677

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Ctcf, Ctcfl

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_3: # seqlets: 1931

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Sp3, Sp5, Sp2, Klf16, Klf5

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_4: # seqlets: 1464

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Foxa1, Foxa2, Foxf2, Foxa3, Foxc1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_5: # seqlets: 1345

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Erf, Etv5, Gabpa, Erg, Elk1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_6: # seqlets: 1109

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Nfic

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_7: # seqlets: 1050

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_8: # seqlets: 1024

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_9: # seqlets: 981

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Nfia, Nfix, Nfib, Nfic

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_10: # seqlets: 874

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Onecut3, Onecut1, Onecut2, Sox8

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_11: # seqlets: 718

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Foxi1, Pbx3, Nfya, Ybx1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_12: # seqlets: 523

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Tcfec, Tcfeb, Bach2, Srebf1, Mitf

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_13: # seqlets: 459

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  9430076C15Rik, Creb3, Atf7, Creb1, Atf2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_14: # seqlets: 443

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Irf1, Prdm1, Stat2, Irf2, Irf4

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_15: # seqlets: 283

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Smarcc2, Tbx2, Zfp143, Zfp523, Six5

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_16: # seqlets: 268

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Mbtps2, Yy1, Sp3, Wt1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_17: # seqlets: 249

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Nr5a2, Nr6a1, Esrrb, Nr5a1, Esrrg

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_18: # seqlets: 104

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Bach1, Nfe2l2, Nfe2, Smarcc1, Fos

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_19: # seqlets: 97

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Gata2, Gata1, Gata6, Gata4, Gata5

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_20: # seqlets: 90

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Sp3, Zfx, Tcfap2d, Zbtb7a, E2f1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  

modisco_report_pipeline(sample_name, modisco_root, mitra_subdir, task_dir, database_name, 
                        importance=False, render=True)

rsync -t -av /srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019/task_202-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_202-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_202-naivegw
Displaying motifs which has negative importances for the cell type

metacluster_0, # patterns: 25, # seqlets: 13139, Negative for: LVR;8wks;D;GEO

• pattern_0: # seqlets: 2738

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_1: # seqlets: 2555

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Glis2, Zbtb7a

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_2: # seqlets: 1667

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Zfp637

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_3: # seqlets: 1423

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Zeb1, Snai2, Mga

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_4: # seqlets: 1370

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Hmg20b, Dbx1, Arid3b, Tlx2, Pou3f4

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_5: # seqlets: 1214

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Hic2, Zbtb7c, Gli3, Gli1, Gli2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_6: # seqlets: 323

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Nfic, Nfia, Nfix, Nfib

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_7: # seqlets: 256

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Nr5a2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_8: # seqlets: 208

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Nr5a2, Nr6a1, Esrrb, Nr2f6, Nr2f2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_9: # seqlets: 196

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Nr5a2, Nr6a1, Nr5a1, Esrrb, Esrrg

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_10: # seqlets: 190

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Rfx2, Arid2, Rfx1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_11: # seqlets: 131

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Cebpb, Cebpd, Cebpg, Cebpa, Cebpe

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_12: # seqlets: 129

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Nr5a2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_13: # seqlets: 82

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Foxd3, Foxm1, Foxj1, Rreb1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_14: # seqlets: 82

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Hsf1, Myc

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_15: # seqlets: 92

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_16: # seqlets: 79

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Pitx2, AC189028.1, Pitx3, Obox5

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_17: # seqlets: 68

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Nfe2l2, Nfe2, Jund, Batf, Fos

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_18: # seqlets: 66

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_19: # seqlets: 57

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_20: # seqlets: 46

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Foxd3

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_21: # seqlets: 52

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_22: # seqlets: 42

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Hsf1, Zfp143

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_23: # seqlets: 37

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Hsf1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_24: # seqlets: 36

  Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores