In [1]:
# Parameters
sample_name = "MEL;D;En"
task_dir = "task_273-naivegw"
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/Naive_modisco2019"
mitra_subdir = "report/tomtom_reports"
#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.
2019-04-07 13:27:20,897 [WARNING] git-lfs not installed

load data from labcluster
In [5]:
report_pipeline(sample_name, modisco_root, mitra_subdir, task_dir, importance=True, render=True)

rsync -t -av /srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019/task_273-naivegw/tomtomout /srv/www/kundaje/msharmin/report/tomtom_reports/task_273-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/tomtom_reports/task_273-naivegw

TF-MoDISco is using the TensorFlow backend.

Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 20, # seqlets: 24937, Positive for: MEL;D;En
In [6]:
report_pipeline(sample_name, modisco_root, mitra_subdir, task_dir, importance=False, render=True)

rsync -t -av /srv/scratch/msharmin/mouse_hem/with_tfd/full_mouse50/Naive_modisco2019/task_273-naivegw/tomtomout /srv/www/kundaje/msharmin/report/tomtom_reports/task_273-naivegw/
chmod -R +755 /srv/www/kundaje/msharmin/report/tomtom_reports/task_273-naivegw
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 22, # seqlets: 9954, Negative for: MEL;D;En
  • pattern_0: # seqlets: 1948 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zbtb7a

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_1: # seqlets: 1822 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_2: # seqlets: 1598 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Zeb1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_3: # seqlets: 873 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_4: # seqlets: 763 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_5: # seqlets: 499 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Erg, Sfpi1, Ets1, ENSMUSG00000044690, Elf5, Bcl11a

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_6: # seqlets: 352 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Runx2, Runx1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_7: # seqlets: 357 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_8: # seqlets: 322 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_9: # seqlets: 267 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Fos, Nfe2l2, Nfe2, Smarcc1, Jund, Batf, Fosb, Bach1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_10: # seqlets: 196 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_11: # seqlets: 176 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_12: # seqlets: 108 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_13: # seqlets: 109 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Foxd3, Foxj1

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_14: # seqlets: 92 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_15: # seqlets: 92 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_16: # seqlets: 83 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_17: # seqlets: 91 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    Nr5a2

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_18: # seqlets: 76 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_19: # seqlets: 45 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_20: # seqlets: 49 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores
  • pattern_21: # seqlets: 36 Cisbp matches (q-value>=0.01) using Tomtom (Full Report) :

    SequenceContrib ScoresHyp_Contrib Scores