In [1]:
# Parameters
hyperparameter_group = "_45k_832"
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 19:35:26,443 [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_832/tomtomout /srv/www/kundaje/msharmin/report/test/task_0-naivegw_45k_832/
chmod -R +755 /srv/www/kundaje/msharmin/report/test/task_0-naivegw_45k_832

TF-MoDISco is using the TensorFlow backend.

Displaying motifs which has positive importances for the cell type
metacluster_1, # patterns: 22, # seqlets: 26641, 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_832/tomtomout /srv/www/kundaje/msharmin/report/test/task_0-naivegw_45k_832/
chmod -R +755 /srv/www/kundaje/msharmin/report/test/task_0-naivegw_45k_832
Displaying motifs which has negative importances for the cell type
metacluster_0, # patterns: 14, # seqlets: 9288, Negative for: MPP;A;CL