# Parameters
sample_name = "wES;LVR;E11.5;D.;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_225-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_225-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 02:42:00,312 [WARNING] git-lfs not installed

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	Liver(E14.5)
Cell Group	ES cells and embryonic tissues
Experiment Name	DHS
Experiment Group	ENCODE

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	86429	50597	15.8503	32048018	4011287	0.1252	3993082	0.1247	11747021	0.3667
rep2	86429	50597	15.4017	30545341	4637723	0.1519	4338846	0.1421	11030209	0.3613

Modelling Metadata

Metric	Value
auPRC	0.5917
Calibrated Recall at 50% FDR	0.183
Number of Positive Examples in Test Data	62305
Number of Negative Examples in Test Data	8008546
Imbalance Ratio in Test Data	0.0077
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
Pbx3
Ctcf
Sp5
Gabpa

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Rest		absent
Tcfec		absent
Smarcc2		absent
Gata6		absent
Mbtps2		absent
Cebpb		absent
Klf2		absent
Nr1h2		absent
Creb3		absent
Nfia		absent
Nfe2l2		absent
Rfx2		absent
Stat2		absent
Hsf1		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Cebpg	absent
Gata2	absent
Tcfeb	absent
Grhl1	absent
Bach1	absent
Zfp143	absent
Yy1	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_225-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_225-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_225-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_1, # patterns: 23, # seqlets: 24482, Positive for: wES;LVR;E11.5;D.;En

• pattern_0: # seqlets: 7174

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

  Ctcf, Ctcfl

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_1: # seqlets: 3859

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

  Sp5, Sp3, Klf16, Klf14, Klf5

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_2: # seqlets: 1779

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

  Pbx3, Foxi1, Nfya, Ybx1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_3: # seqlets: 1711

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

  Gabpa, Erg, Erf, Ets1, Ets2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_4: # seqlets: 1528

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_5: # seqlets: 1071

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

  Gata6, Gata5, Gata1, Gata3, Gata2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_6: # seqlets: 916

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

  Klf2, Klf5, Sp5, Klf1, Klf4

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_7: # seqlets: 835

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

  Mbtps2, Sp3, Yy1, Wt1, E2f1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_8: # seqlets: 755

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

  Smarcc2, Tbx2, Zfp143, Zfp523, Six5

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_9: # seqlets: 667

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

  Cebpb, Cebpd, Cebpa, Cebpg, Cebpe

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_10: # seqlets: 594

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

  Creb3, Atf7, Jdp2, 9430076C15Rik, Atf2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_11: # seqlets: 560

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

  Tcfec, Tcfeb, Bach2, Mitf, Tcfe3

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_12: # seqlets: 555

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

  Rfx2, Rfx1, Arid2, Rfx4, Rfx7

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_13: # seqlets: 553

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

  Nfe2l2, Nfe2, Bach1, Fos, Smarcc1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_14: # seqlets: 372

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_15: # seqlets: 324

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

  Nr1h2, Pparg, Hnf4g, Ppard, Nr4a3

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_16: # seqlets: 250

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_17: # seqlets: 235

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

  Hsf1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_18: # seqlets: 181

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

  Gabpa, Erf, Sp3, Etv5, Fev

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_19: # seqlets: 163

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

  Rest

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_20: # seqlets: 144

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

  Gabpa, Sp3, Creb1, E4f1, Zfx

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_21: # seqlets: 134

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

  Nfia, Nfix, Nfib, Nfic, Meis1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_22: # seqlets: 122

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

  Stat2, Irf1, Irf4, Irf5, Prdm1

  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_225-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_225-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_225-naivegw
Displaying motifs which has negative importances for the cell type

metacluster_0, # patterns: 23, # seqlets: 9914, Negative for: wES;LVR;E11.5;D.;En

• pattern_0: # seqlets: 1544

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

  Zeb1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_1: # seqlets: 1513

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

  Dbx1, Lhx3, Lhx5, Arid3b, Tlx2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_2: # seqlets: 1142

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

  Zbtb7a, Rreb1, Sp3, Wt1, Klf16

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_3: # seqlets: 1123

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

  Gata2, Gata6, Gata4, Gata1, Gata3

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_4: # seqlets: 1056

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

  Zbtb7a

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_5: # seqlets: 831

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

  Pbx2, Hoxa9, Onecut1, Onecut3

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_6: # seqlets: 680

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

  Tcf15, Zfp238, Tcfap4, Tal1, Bhlha15

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_7: # seqlets: 306

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

  Hnf4g, Nr1h2, Pparg, Nr1h4, Ppard

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_8: # seqlets: 261

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

  Sox9, Sox6, Sox4, Sox17, Sox3

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_9: # seqlets: 202

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

  Ppara, Nr1h2, Rxra, Nr4a2, Hnf4g

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_10: # seqlets: 194

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_11: # seqlets: 187

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

  Egr2, Tcf4, Tcf3, Rreb1, Sp3

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_12: # seqlets: 142

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

  Klf1, Klf2, Klf4, Klf8, Klf3

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_13: # seqlets: 142

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

  Nr5a2, Pitx2, AC189028.1, Pitx3, Obox5

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_14: # seqlets: 121

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

  Foxd3, Foxj1, Foxm1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_15: # seqlets: 101

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_16: # seqlets: 75

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

  Foxb1, Foxf2, Foxc1, Foxc2, Foxl1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_17: # seqlets: 67

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

  Tbpl2, Foxa3, Foxb1, Foxc1, Foxl1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_18: # seqlets: 53

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

  Nr5a2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_19: # seqlets: 52

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_20: # seqlets: 41

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

  Tcf4

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_21: # seqlets: 46

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

  Pitx2, AC189028.1, Pitx3, Obox5

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_22: # seqlets: 35

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores