In [1]:
# Parameters
hyperparameter_group = "_20k_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 19:28:19,454 [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_20k_610/tomtomout /srv/www/kundaje/msharmin/report/test/task_0-naivegw_20k_610/
chmod -R +755 /srv/www/kundaje/msharmin/report/test/task_0-naivegw_20k_610

TF-MoDISco is using the TensorFlow backend.

Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 21, # seqlets: 12035, 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_20k_610/tomtomout /srv/www/kundaje/msharmin/report/test/task_0-naivegw_20k_610/
chmod -R +755 /srv/www/kundaje/msharmin/report/test/task_0-naivegw_20k_610
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 14, # seqlets: 3125, Negative for: MPP;A;CL
  • pattern_0: # seqlets: 743 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 639 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 499 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 380 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Erg, Ets1, ENSMUSG00000044690, Elf5, Fev, Elf3, Ehf

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 227 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Runx1, Runx2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 192 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 114 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 57 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 54 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Hsf1, Myc

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 52 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 45 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 42 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 43 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 38 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores