In [1]:
# Parameters
hyperparameter_group = "_45k_610"
sample_name = "MPP_A_CL"
In [2]:
try:
    reload  # Python 2.7
except NameError:
    try:
        from importlib import reload  # Python 3.4+
    except ImportError:
        from imp import reload  # Python 3.0 - 3.3
In [3]:
modisco_root = "/srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/modisco2019"
mitra_subdir = "report/test"
task_idx = 0
sample_name = "MPP;A;CL"
task_dir = "task_{0}-naivegw{1}".format(task_idx, hyperparameter_group)
In [4]:
from matlas.modisco_report import report_pipeline
#modisco_report.run_pipeline(sample_name, prepare=False, render=False)

Using TensorFlow backend.
2019-02-26 19:39:22,065 [WARNING] git-lfs not installed
In [5]:
report_pipeline(sample_name, modisco_root, mitra_subdir, task_dir, importance=True)

rsync -t -av /srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/modisco2019/task_0-naivegw_45k_610/tomtomout /srv/www/kundaje/msharmin/report/test/task_0-naivegw_45k_610/
chmod -R +755 /srv/www/kundaje/msharmin/report/test/task_0-naivegw_45k_610

TF-MoDISco is using the TensorFlow backend.

Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 27, # seqlets: 25101, Positive for: MPP;A;CL
In [6]:
report_pipeline(sample_name, modisco_root, mitra_subdir, task_dir, importance=False)

rsync -t -av /srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/modisco2019/task_0-naivegw_45k_610/tomtomout /srv/www/kundaje/msharmin/report/test/task_0-naivegw_45k_610/
chmod -R +755 /srv/www/kundaje/msharmin/report/test/task_0-naivegw_45k_610
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 27, # seqlets: 8733, Negative for: MPP;A;CL
  • pattern_0: # seqlets: 1353 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1262 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zbtb7b, Glis1, Zic5

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 947 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 663 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 598 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 567 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 500 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Ets1, Erg, Etv5, Fli1, Etv6, Elk3, Etv1, Elk1, Etv4, Etv3, Gm5454, Gm4881, Fev, Elk4, Erf, Ets2, ENSMUSG00000044690

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 467 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tcf15, Msc, Zfp238, Tcf21, Tal1, Neurog1, Bhlha15, Neurod2, Olig1, Olig2, Atoh8

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 462 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Runx1, Runx2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 270 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Klf15, Sp3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 184 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxd3, Foxp4, Foxa3, Foxj3, Foxn3, Foxm1, Gm5294, Foxj1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 164 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 165 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 147 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 137 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 100 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxd3

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 99 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 90 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 81 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 79 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 77 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_21: # seqlets: 67 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_22: # seqlets: 60 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Tbpl2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_23: # seqlets: 54 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_24: # seqlets: 43 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zfp263

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_25: # seqlets: 42 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_26: # seqlets: 55 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores