# Parameters
sample_name = "STMCH;P0;D;En"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_264-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_264-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 04:37:12,024 [WARNING] git-lfs not installed

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	stomach(P0)
Cell Group	Other 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	174433	121637	6.4419	120853885	10636266	0.088	7502125	0.0621	41576855	0.3441
rep2	181904	121637	5.6203	163088440	NA	NA	NA	NA	NA	NA

Modelling Metadata

Metric	Value
auPRC	0.5673
Calibrated Recall at 50% FDR	0.242
Number of Positive Examples in Test Data	82943
Number of Negative Examples in Test Data	7987908
Imbalance Ratio in Test Data	0.0103
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
Foxa2
Ehf
Creb3
Hnf4g
Ctcf
Rest

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Nfia		absent
Grhl1		absent
Sp3		absent
Foxb1		absent
Mef2d		absent
Smarcc2		absent
Mbtps2		absent
Sp2		absent
Klf12		absent
Tcfeb		absent
Gata2		absent
Rfx1		absent
Irf4		absent
Fos		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Tcfcp2	absent
Klf7	absent
Smarcc1	absent
Gata6	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_264-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_264-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_264-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_1, # patterns: 24, # seqlets: 23236, Positive for: STMCH;P0;D;En

• pattern_0: # seqlets: 4282

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

  Ctcf, Ctcfl

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_1: # seqlets: 2420

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

  Sp2, Sp3, Klf5, Sp5, Klf16

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_2: # seqlets: 2223

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

  Klf12, Klf7, Klf8, Klf2, Klf4

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_3: # seqlets: 2216

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

  Ehf, Elf5, Elf1, Elk1, Nr2c2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_4: # seqlets: 1367

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

  Foxa2, Foxa1, Foxf2, Foxa3, Foxc1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_5: # seqlets: 1130

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

  Creb3, 9430076C15Rik, Creb1, Atf2, Atf7

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_6: # seqlets: 1070

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

  Nfia, Nfib, Nfix, Nfic

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_7: # seqlets: 1046

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

  Pbx3, Foxi1, Nfya, Ybx1, Dux

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_8: # seqlets: 972

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

  Sp3, Zfx

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_9: # seqlets: 870

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

  Fos, Smarcc1, Jund, Fosb, Nfe2l2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_10: # seqlets: 861

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

  Foxb1, Tbpl2, Foxc1, Foxc2, Foxa3

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_11: # seqlets: 679

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

  Hnf4g, Nr1h2, Pparg

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_12: # seqlets: 606

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

  Grhl1, Tcfcp2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_13: # seqlets: 542

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

  Irf4, Irf1, Stat2, Prdm1, Irf5

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_14: # seqlets: 483

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_15: # seqlets: 463

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

  Tcfeb, Bach2, Tcfec, Usf2, Mitf

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_16: # seqlets: 426

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

  Smarcc2, Tbx2, Zfp143, Zfp523, Six5

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_17: # seqlets: 375

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

  Gata2, Gata4, Gata1, Mecom, Gata6

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_18: # seqlets: 360

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

  Rfx1, Rfx2, Arid2, Rfx4, Rfx7

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_19: # seqlets: 260

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_20: # seqlets: 238

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

  Mbtps2, Yy1, Sp3, Wt1, E2f1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_21: # seqlets: 144

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

  Sp3

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_22: # seqlets: 127

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

  Mef2d, Mef2b, Mef2a, Mef2c

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_23: # seqlets: 76

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

  Rest

  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_264-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_264-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_264-naivegw
Displaying motifs which has negative importances for the cell type

metacluster_0, # patterns: 26, # seqlets: 11280, Negative for: STMCH;P0;D;En

• pattern_0: # seqlets: 2004

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_1: # seqlets: 1829

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

  Gata2, Gata6, Gata4, Gata3, Gata1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_2: # seqlets: 1803

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

  Zbtb7b, Zbtb7a, Zic5, Glis2, Glis1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_3: # seqlets: 957

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

  Nr1h2, Ppara, Hnf4g, Nr6a1, Pparg

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_4: # seqlets: 647

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

  Foxa3, Foxa1, Foxf2, Foxa2, Foxc1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_5: # seqlets: 576

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_6: # seqlets: 488

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_7: # seqlets: 425

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

  Foxa1, Foxb1, Foxc2, Foxc1, Foxa3

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_8: # seqlets: 421

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

  Erg, Ets1, ENSMUSG00000044690, Fev, Elf5

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_9: # seqlets: 383

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

  Klf1, Klf3, Klf2, Klf4, Klf8

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_10: # seqlets: 359

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

  Zeb1, Tcf4, Mga, Mesp2, Tbx4

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_11: # seqlets: 348

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

  Nfe2l2, Nfe2, Jund, Fos, Batf

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_12: # seqlets: 148

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_13: # seqlets: 132

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_14: # seqlets: 118

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

  Nr5a2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_15: # seqlets: 97

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

  Pitx2, AC189028.1, Pitx3, Obox5

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_16: # seqlets: 82

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

  AC189028.1, Pitx2, Obox5, Pitx3, Maz

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_17: # seqlets: 78

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_18: # seqlets: 73

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_19: # seqlets: 68

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

  Hsf1, Zfp143

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_20: # seqlets: 56

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_21: # seqlets: 50

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

  Ctcf

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_22: # seqlets: 39

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

  Zfp637

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_23: # seqlets: 34

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

  Nr5a2, Esrrb, Nr6a1, Nr5a1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_24: # seqlets: 35

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_25: # seqlets: 30

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

  Nr5a2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores