# Parameters
sample_name = "CN_PHT_RCPTR;A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_154-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_154-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 22:55:14,585 [WARNING] git-lfs not installed

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	WT cone photoreceptors
Cell Group	Neural Cells and Tissues
Experiment Name	ATAC
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	148954	114410	21.7676	30932642	9609091	0.3108	6967520	0.2254	11652073	0.3769
rep2	148954	114410	23.1075	27082405	8207576	0.3033	6123020	0.2262	10108202	0.3735

Modelling Metadata

Metric	Value
auPRC	0.6428
Calibrated Recall at 50% FDR	0.235
Number of Positive Examples in Test Data	117598
Number of Negative Examples in Test Data	7953253
Imbalance Ratio in Test Data	0.0146
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
Mbtps2
Ctcf
Crx

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Rora		absent
Atoh1		absent
Rfx8		absent
Jdp2		absent
Irf1		absent
Mef2d		absent
Foxi1		absent
Bach2		absent
Tbpl2		absent
Ets1		absent
Smarcc2		absent
Sp3		absent
Hsf1		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Elk3	absent
Zfp143	absent
Rax	absent
Sp2	absent
Maz	absent
Tcfeb	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_154-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_154-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_154-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_1, # patterns: 19, # seqlets: 22424, Positive for: CN_PHT_RCPTR;A;GEO

• pattern_0: # seqlets: 6425

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

  Ctcf, Ctcfl

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_1: # seqlets: 5502

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

  Crx, Dmbx1, Otx2, Gsc2, Otx1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_2: # seqlets: 2035

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_3: # seqlets: 1331

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

  Sp3, Klf16, Sp5, Sp1, Klf5

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_4: # seqlets: 1178

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

  Foxi1, Pbx3, Nfya, Ybx1, Dux

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_5: # seqlets: 1059

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

  Ets1, Gabpa, Elk3, Etv4, Erf

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_6: # seqlets: 832

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

  Mbtps2, Yy1, Wt1, Sp3

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_7: # seqlets: 749

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

  Sp3, Sp2, Zfp148, Zfp281, Zbtb7a

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_8: # seqlets: 657

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

  Smarcc2, Tbx2, Zfp143, Zfp523, Six5

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_9: # seqlets: 594

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

  Jdp2, Atf7, Atf2, Creb1, Creb3

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_10: # seqlets: 540

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

  Bach2, Mitf, Tcfeb, Tcfe3, Tcfec

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_11: # seqlets: 353

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

  Mef2d, Mef2b, Mef2c, Mef2a

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_12: # seqlets: 321

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

  Ctcf, Ctcfl, Thrb

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_13: # seqlets: 289

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

  Atoh1, Neurod1, Neurod2, Tal1, Bhlhe22

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_14: # seqlets: 190

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

  Rora

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_15: # seqlets: 125

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

  Rfx8, Rfx3, Rfx5, Rfx7, Rfx4

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_16: # seqlets: 96

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

  Tbpl2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_17: # seqlets: 66

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

  Irf1, Prdm1, Stat2, Irf2, Bcl11a

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_18: # seqlets: 82

  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_154-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_154-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_154-naivegw
Displaying motifs which has negative importances for the cell type

metacluster_0, # patterns: 30, # seqlets: 10686, Negative for: CN_PHT_RCPTR;A;GEO

• pattern_0: # seqlets: 1741

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

  Glis2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_1: # seqlets: 1252

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_2: # seqlets: 1071

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

  Tbp, Ahctf1, Hmg20b, Onecut1, Zfp637

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_3: # seqlets: 779

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_4: # seqlets: 624

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_5: # seqlets: 602

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

  Hsf1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_6: # seqlets: 560

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

  Hmg20b, Arid3b, Dbx1, Phf21a, Pou3f4

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_7: # seqlets: 399

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

  Snai2, Zeb1, Id4, Mesp2, Twist1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_8: # seqlets: 398

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

  Bcl6

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_9: # seqlets: 348

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_10: # seqlets: 339

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

  Gli1, Gli3, Gli2, Zbtb7b

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_11: # seqlets: 336

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_12: # seqlets: 330

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

  Zfp238, Tcf4, Bhlha15, Tcf21, Twist2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_13: # seqlets: 323

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

  Crx, Dmbx1, Otx1, Otx2, Pitx2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_14: # seqlets: 318

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

  Nr5a2, Pitx2, AC189028.1, Pitx3, Obox5

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_15: # seqlets: 276

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

  Hmg20b

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_16: # seqlets: 185

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

  Esrrb, Nr5a1, Nr5a2, Esrrg, Nr6a1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_17: # seqlets: 115

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

  Nr5a2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_18: # seqlets: 100

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

  Nr5a2, Esrrb, Nr6a1, Nr5a1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_19: # seqlets: 92

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_20: # seqlets: 83

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

  Ahctf1, Tbp

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_21: # seqlets: 67

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_22: # seqlets: 52

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

  Zeb1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_23: # seqlets: 51

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

  Bach1, Fosb

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_24: # seqlets: 48

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_25: # seqlets: 44

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_26: # seqlets: 46

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

  Nr5a2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_27: # seqlets: 36

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_28: # seqlets: 34

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

  Ctcfl, Sp3, E2f1, Ctcf, Zfx

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_29: # seqlets: 37

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

  Nr5a2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores