# Parameters
sample_name = "wES;GRM;E16.5;A;GEO"
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019"
mitra_subdir = "report/version2"
task_dir = "task_179-naivegw"
database_name = "CISBP"
perf_file = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/fineFactorized/task_179-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 00:21:50,141 [WARNING] git-lfs not installed

display_metadata(sample_name, perf_file, reportfile, sheetname)

Sample Information

MetaData Name	Description
Cell type	E16.5 sorted germ cells(wt)
Cell Group	ES cells and embryonic 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	209073	119719	7.2165	90508387	10187316	0.1126	5138199	0.0568	28688474	0.317

Modelling Metadata

Metric	Value
auPRC	0.4588
Calibrated Recall at 50% FDR	0.343
Number of Positive Examples in Test Data	80019
Number of Negative Examples in Test Data	7990832
Imbalance Ratio in Test Data	0.0099
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

Unique TF-MoDISco Motifs

Motif Name	Modisco	Homer
Yy1		absent
Smarcc2		absent
Sp2		absent
Rfx5		absent
Ets1		absent
Twist1		absent
Tcfeb		absent
Smad2		absent
Ctcfl		absent
Mbtps2		absent
Zfx		absent
Sp3		absent
Rfx1		absent
Maz		absent
Jdp2		absent

Unique Homer Motifs

Motif Name	Modisco	Homer
Rfx8	absent
E4f1	absent
Klf5	absent
Zfp143	absent
Ovol1	absent
Gabpa	absent
Klf1	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_179-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_179-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_179-naivegw
Displaying motifs which has positive importances for the cell type

metacluster_0, # patterns: 34, # seqlets: 13192, Positive for: wES;GRM;E16.5;A;GEO

• pattern_0: # seqlets: 1784

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

  Sp3, Sp5, Klf5, Sp2, Klf16

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_1: # seqlets: 1525

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

  Pbx3, Foxi1, Nfya, Ybx1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_2: # seqlets: 1481

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

  Sp2, Sp3, Klf16, Sp8, Sp5

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_3: # seqlets: 1366

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

  Sp3, Zfx, Tcfap2d, E2f1, Zbtb7a

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_4: # seqlets: 1002

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

  Sp3, E2f1, Tcfap2d, Zfx, Wt1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_5: # seqlets: 869

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

  Sp3, Sp2, Zbtb7a, E2f1, Wt1

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_6: # seqlets: 618

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

  Ctcfl, Ctcf

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_7: # seqlets: 610

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

  Ets1, Nr2c2, Erf, Gabpa, Elk3

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_8: # seqlets: 550

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

  Rfx5, Zfp740

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_9: # seqlets: 430

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

  Tcfeb, Bach2, Tcfec, Mitf, Tcfe3

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_10: # seqlets: 346

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

  Rfx1, Arid2, Rfx2, Rfx4, Rfx7

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_11: # seqlets: 321

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

  Smarcc2, Tbx2, Zfp143, Zfp523, Six5

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_12: # seqlets: 279

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

  Zfx, Sp3

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_13: # seqlets: 277

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

  Jdp2, Creb3, Atf7, 9430076C15Rik, Atf2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_14: # seqlets: 205

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_15: # seqlets: 197

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

  Mbtps2, Yy1, Sp3, Wt1, Zbtb7a

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_16: # seqlets: 138

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_17: # seqlets: 129

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_18: # seqlets: 118

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_19: # seqlets: 114

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

  Yy1, Mbtps2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_20: # seqlets: 91

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_21: # seqlets: 77

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_22: # seqlets: 75

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_23: # seqlets: 88

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_24: # seqlets: 63

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

  Maz, Gli3, Gli1, Rbpj, Bcl6

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_25: # seqlets: 81

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

  Yy1, Mbtps2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_26: # seqlets: 50

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

  Twist1, Hic2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_27: # seqlets: 46

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

  Smad2

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_28: # seqlets: 45

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_29: # seqlets: 41

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_30: # seqlets: 38

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_31: # seqlets: 36

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_32: # seqlets: 47

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

  Sequence

  

  Contrib Scores

  

  Hyp_Contrib Scores

  
• pattern_33: # seqlets: 55

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

  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_179-naivegw/cisbp_tomtomout /srv/www/kundaje/msharmin/report/version2/task_179-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/version2/task_179-naivegw

No motifs with negative importance