# Parameters
sample_name = "ES;MEF;A;CL"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_51-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_51-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.
2019-07-22 17:39:14,644 [WARNING] git-lfs not installed

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	MEFs
Cell Group	ES cells and embryonic tissues
Experiment Name	ATAC
Experiment Group	Casellas Lab

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	171014	109817	11.4467	53388578	10460589	0.196	5967968	0.1118	22517940	0.4219

Modelling Metadata

Metric	Value
auPRC	0.6632
Calibrated Recall at 50% FDR	0.192
Number of Positive Examples in Test Data	124907
Number of Negative Examples in Test Data	7945944
Imbalance Ratio in Test Data	0.0155
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
Ctcf
Runx2
Sp2
Creb3
Fos
Smarcc2

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Bhlha15		absent
Foxi1		absent
Srf		absent
Bach2		absent
Nfia		absent
Mbtps2		absent
Cebpb		absent
Mef2a		absent
Sp3		absent
Rfx1		absent
Erg		absent
Hsf1		absent
Irf1		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Elk4	absent
Hes7	absent
Pbx3	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_51-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_51-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_51-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_1, # patterns: 23, # seqlets: 21241, Positive for: ES;MEF;A;CL

• pattern_0: # seqlets: 3789

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

  Fos, Jund, Fosb, Smarcc1, Nfe2l2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_1: # seqlets: 3301

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

  Ctcf, Ctcfl

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_2: # seqlets: 2961

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

  Sp2, Sp3, Klf5, Maz, Klf16

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_3: # seqlets: 2013

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_4: # seqlets: 1679

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

  Erg, Ets1, Erf, Gabpa, Etv5

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_5: # seqlets: 1219

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

  Creb3, 9430076C15Rik, Batf3, Atf7, Atf2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_6: # seqlets: 1031

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

  Foxi1, Pbx3, Nfya, Ybx1, Dux

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_7: # seqlets: 732

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_8: # seqlets: 687

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

  Nfia, Nfib, Nfix, Nfic

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_9: # seqlets: 669

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

  Runx2, Runx1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_10: # seqlets: 476

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

  Rfx1, Rfx2, Arid2, Rfx4, Rfx7

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_11: # seqlets: 373

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

  Cebpb, Cebpd, Cebpg, Cebpa, Cebpe

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_12: # seqlets: 347

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

  Smarcc2, Tbx2, Zfp143, Zfp523, Six5

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_13: # seqlets: 341

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

  Srf

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_14: # seqlets: 295

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

  Bach2, Tcfec, Tcfeb, Mitf, Tcfe3

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_15: # seqlets: 263

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

  Mbtps2, Yy1, Sp3, Wt1, E2f1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_16: # seqlets: 244

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

  Bhlha15, Tcf21, Msc, Olig2, Lhx3

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_17: # seqlets: 244

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

  Mef2a, Mef2c, Mef2d, Mef2b

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_18: # seqlets: 153

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

  Irf1, Prdm1, Stat2, Irf2, Irf4

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_19: # seqlets: 147

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_20: # seqlets: 126

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

  Sp3, Wt1, E2f1, Zfx, Egr4

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_21: # seqlets: 86

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

  Sp3, E2f1, Zfx

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_22: # seqlets: 65

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

  Hsf1

  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_51-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_51-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_51-naivegw
Displaying motifs which has negative importances for the cell type

metacluster_0, # patterns: 23, # seqlets: 12505, Negative for: ES;MEF;A;CL

• pattern_0: # seqlets: 1830

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

  Zbtb7b, Zbtb7a, Glis2, Zic5, Glis1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_1: # seqlets: 1793

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

  Zeb1, Snai2, Id4, Mesp2, Twist1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_2: # seqlets: 1688

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

  Hmg20b, Dbx1, Tlx2, Arid3b, Pit1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_3: # seqlets: 1163

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

  Dbx1, Arid3b, Tlx2, Sebox, Lhx3

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_4: # seqlets: 848

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

  Rfx2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_5: # seqlets: 758

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_6: # seqlets: 609

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

  Ppara, Nr4a1, Nr1h2, Esrrg, Esrra

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_7: # seqlets: 568

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

  Onecut3, Onecut1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_8: # seqlets: 531

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

  Nfe2l2, Nfe2, Jund, Batf, Fos

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_9: # seqlets: 524

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

  Gli2, Gli3, Gli1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_10: # seqlets: 490

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_11: # seqlets: 398

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

  Nr5a2, Nr6a1, Esrrb

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_12: # seqlets: 281

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_13: # seqlets: 249

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_14: # seqlets: 158

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

  Bcl6, Maz, Sfpi1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_15: # seqlets: 156

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_16: # seqlets: 93

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_17: # seqlets: 96

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

  Nr5a2, Pitx2, AC189028.1, Pitx3

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_18: # seqlets: 79

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_19: # seqlets: 49

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_20: # seqlets: 54

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_21: # seqlets: 47

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_22: # seqlets: 43

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores