In [2]:
from matlas.matches import DenovoAitac
motif_name = 'REST'
aitacdir = "/mnt/lab_data2/msharmin/oc-atlas/DanSkinData/fold_a_alex/{}".format(motif_name)
ob = DenovoAitac(aitacdir)
# ob.fetch_tomtom_matches(
# meme_db="/mnt/lab_data/kundaje/users/msharmin/annotations/HOCOMOCOv11_core_pwms_HUMAN_mono.renamed.nonredundant.annotated.meme",
# database_name="HOCOMOCO.nonredundant.annotated",
# save_report=True, tomtom_dir= "{0}/{1}_tomtomout".format(aitacdir, "HOCOMOCO.nonredundant.annotated"))
ob.load_matched_motifs(database_name="HOCOMOCO.nonredundant.annotated")
ob.get_motif_per_celltype(match_threshold=0.05, database_name="HOCOMOCO.nonredundant.annotated")
pattern_tab, pattern_dict = ob.visualize_pattern_table('Aitac')
tf_tab, tf_dict = ob.visualize_tf_table("Aitac")
In [3]:
from vdom.helpers import (b, summary, details)
from IPython.display import display
display(details(summary('Click here for ', b('Denovo Patterns'), ' by ', b('{}'.format('Aitac')),
' in ', b(motif_name),
": #{}".format(len(pattern_dict)),
), pattern_tab))
Click here for Denovo Patterns by Aitac in REST: #64
| Pattern Name | TF Name(s) | Aitac |
|---|---|---|
| filter0 |  | |
| filter1 |  | |
| filter2 |  | |
| filter3 |  | |
| filter4 |  | |
| filter5 |  | |
| filter6 |  | |
| filter7 |  | |
| filter8 |  | |
| filter9 |  | |
| filter10 |  | |
| filter11 |  | |
| filter12 |  | |
| filter13 |  | |
| filter14 |  | |
| filter15 |  | |
| filter16 |  | |
| filter17 |  | |
| filter18 |  | |
| filter19 |  | |
| filter20 |  | |
| filter21 |  | |
| filter22 |  | |
| filter23 |  | |
| filter24 |  | |
| filter25 |  | |
| filter26 |  | |
| filter27 |  | |
| filter28 |  | |
| filter29 |  | |
| filter30 |  | |
| filter31 |  | |
| filter32 |  | |
| filter33 |  | |
| filter34 |  | |
| filter35 |  | |
| filter36 |  | |
| filter37 |  | |
| filter38 |  | |
| filter39 |  | |
| filter40 |  | |
| filter41 |  | |
| filter42 |  | |
| filter43 |  | |
| filter44 |  | |
| filter45 |  | |
| filter46 |  | |
| filter47 |  | |
| filter48 |  | |
| filter49 |  | |
| filter50 |  | |
| filter51 |  | |
| filter52 |  | |
| filter53 |  | |
| filter54 |  | |
| filter55 |  | |
| filter56 |  | |
| filter57 |  | |
| filter58 |  | |
| filter59 |  | |
| filter60 |  | |
| filter61 |  | |
| filter62 |  | |
| filter63 |  |
In [4]:
display(details(summary('Click here for ', b('Motifs'), ' by ', b('{}'.format('Aitac')),
' in ', b(motif_name),
": #{}".format(len(tf_dict)),
), tf_tab))
In [ ]: