# Filepaths and Hard-coded Defaults
proj_root = "/users/kcochran/projects/procap_models/"
sequence_path = proj_root + "genomes/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta"
chrom_sizes = proj_root + "genomes/hg38.chrom.sizes.withrRNA"
in_window = 2114
out_window = 1000
# stuff to get from config file
with open("2022-07-05_09-52-52_run1_modisco_config.txt") as config_f:
config_dict = {line.split()[0] : line.strip().split()[1] for line in config_f}
modisco_out_path = config_dict["modisco_out_path"]
scoring_type = config_dict["scoring_type"]
score_center_size = int(config_dict["score_center_size"])
profile_display_center_size = int(config_dict["profile_display_center_size"])
# digest what's in config file
assay_type, model_type, cell, accession, modisco_dir_base = modisco_out_path.split("/")[-5:]
ts_part1, ts_part2, run_str, _ = modisco_dir_base.split("_")
timestamp = ts_part1 + "_" + ts_part2
run = int(run_str.replace("run", ""))
print(modisco_out_path)
print("cell_type:", cell, accession)
print("timestamp:", timestamp)
print("run:", run)
print("scoring_type:", scoring_type)
print("score_center_size:", score_center_size)
print("profile_display_center_size:", profile_display_center_size)
/users/kcochran//projects/procap_models/modisco_out/procap/bpnetlite_basic_v2/MCF10A/ENCSR799DGV/2022-07-05_09-52-52_run1_modisco cell_type: MCF10A ENCSR799DGV timestamp: 2022-07-05_09-52-52 run: 1 scoring_type: counts score_center_size: 1000 profile_display_center_size: 400
data_dir = proj_root + "/data/procap/processed/" + cell + "/" + accession + "/"
plus_bw_path = data_dir + "final.5prime.pos.bigWig"
minus_bw_path = data_dir + "final.5prime.neg.bigWig"
val_peak_path = data_dir + "peaks_uni_and_bi_train_and_val.bed.gz"
val_save_dir = proj_root + "model_out/" + assay_type + "/" + model_type + "/" + cell + "/" + accession + "/"
val_save_path = val_save_dir + timestamp + "_run" + str(run) + "_train_and_val"
attr_save_path = val_save_dir.replace("model_out", "deepshap_out") + timestamp + "_run" + str(run) + "_deepshap"
if not modisco_out_path.endswith("/"):
modisco_out_path = modisco_out_path + "/"
# task-specific filepaths
import os
assert scoring_type in ["profile", "counts"], scoring_type
if scoring_type == "profile":
scores_path = attr_save_path + "_prof.npy"
onehot_scores_path = attr_save_path + "_prof_onehot.npy"
modisco_obj_path = modisco_out_path + "results_allChroms_prof_slice500.hdf5"
seqlet_path = modisco_out_path + "seqlets_prof.txt"
else:
scores_path = attr_save_path + "_count.npy"
onehot_scores_path = attr_save_path + "_count_onehot.npy"
modisco_obj_path = modisco_out_path + "results_allChroms_count_slice500.hdf5"
seqlet_path = modisco_out_path + "seqlets_count.txt"
assert(os.path.exists(scores_path)), scores_path
assert(os.path.exists(onehot_scores_path)), onehot_scores_path
# Imports, Plotting Defaults
import matplotlib.pyplot as plt
import matplotlib.font_manager as font_manager
plot_params = {
"figure.titlesize": 22,
"axes.titlesize": 22,
"axes.labelsize": 20,
"legend.fontsize": 18,
"xtick.labelsize": 16,
"ytick.labelsize": 16,
"font.weight": "bold"
}
plt.rcParams.update(plot_params)
from IPython.display import display
import tqdm
tqdm.tqdm_notebook()
import numpy as np
from view_modisco_results_utils import *
/users/kcochran/miniconda3/envs/procap/lib/python3.7/site-packages/ipykernel_launcher.py:19: TqdmDeprecationWarning: This function will be removed in tqdm==5.0.0 Please use `tqdm.notebook.tqdm` instead of `tqdm.tqdm_notebook`
# Load in True Profiles and Sequences
import sys
sys.path.append('../1_train_models')
from data_loading import extract_peaks
one_hot_seqs, true_profs = extract_peaks(sequence_path,
plus_bw_path, minus_bw_path, val_peak_path, in_window, out_window,
max_jitter=0, verbose=True)
one_hot_seqs = one_hot_seqs.swapaxes(1,2)
one_hot_seqs = one_hot_seqs[:, (in_window // 2 - score_center_size // 2):(in_window // 2 + score_center_size // 2), :]
Reading FASTA: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 24/24 [00:14<00:00, 1.63it/s] Loading Peaks: 52007it [01:16, 680.14it/s]
# Load in Coordinates of Examples
coords = load_coords(val_peak_path, in_window)
# Import SHAP scores, predicted profiles
hyp_scores = np.load(scores_path).swapaxes(1,2)
hyp_scores = hyp_scores[:, (in_window // 2 - score_center_size // 2):(in_window // 2 + score_center_size // 2), :]
pred_profs = np.exp(np.load(val_save_path + ".profs.npy"))
# Load modisco results object
tfm_obj = import_tfmodisco_results(modisco_obj_path, hyp_scores, one_hot_seqs)
motif_pfms, motif_hcwms, motif_cwms, \
motif_pfms_short, num_seqlets, \
motif_seqlets, num_metaclusters = plot_all_metaclusters(tfm_obj, one_hot_seqs, hyp_scores,
true_profs, pred_profs, coords,
in_window, out_window,
score_center_size,
profile_display_center_size)
14601 seqlets
Sequence (PFM) | |
Hypothetical contributions (hCWM) | |
Actual contributions (CWM) |
13270 seqlets
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12697 seqlets
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7051 seqlets
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5554 seqlets
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3986 seqlets
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2896 seqlets
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2753 seqlets
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2447 seqlets
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2250 seqlets
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1247 seqlets
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1103 seqlets
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1069 seqlets
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990 seqlets
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883 seqlets
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840 seqlets
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825 seqlets
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802 seqlets
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753 seqlets
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689 seqlets
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652 seqlets
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485 seqlets
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459 seqlets
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426 seqlets
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423 seqlets
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411 seqlets
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265 seqlets
Sequence (PFM) | |
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262 seqlets
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244 seqlets
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195 seqlets
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169 seqlets
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49 seqlets
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37 seqlets
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25 seqlets
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109 seqlets
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84 seqlets
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47 seqlets
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41 seqlets
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28 seqlets
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24 seqlets
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Actual contributions (CWM) |
run_and_plot_tomtom(modisco_out_path, motif_pfms, motif_hcwms, motif_pfms_short, num_metaclusters)
The output directory '/users/kcochran//projects/procap_models/modisco_out/procap/bpnetlite_basic_v2/MCF10A/ENCSR799DGV/2022-07-05_09-52-52_run1_modisco/tomtom' already exists. Its contents will be overwritten. Processing query 1 out of 34 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.972668 Processing query 2 out of 34 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.9855 Processing query 3 out of 34 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.985757 Processing query 4 out of 34 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.957616 Processing query 5 out of 34 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=1 Processing query 6 out of 34 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.996804 Processing query 7 out of 34 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.993429 Processing query 8 out of 34 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.998859 Processing query 9 out of 34 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.969023 Processing query 10 out of 34 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.989097 Processing query 11 out of 34 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=1 Processing query 12 out of 34 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=1 Processing query 13 out of 34 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.97084 Processing query 14 out of 34 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.995476 Processing query 15 out of 34 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=1 Processing query 16 out of 34 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.98076 Processing query 17 out of 34 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.946735 Processing query 18 out of 34 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.966958 Processing query 19 out of 34 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.970059 Processing query 20 out of 34 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.974796 Processing query 21 out of 34 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.977279 Processing query 22 out of 34 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.999515 Processing query 23 out of 34 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.966675 Processing query 24 out of 34 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.950242 Processing query 25 out of 34 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.983756 Processing query 26 out of 34 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.998346 Processing query 27 out of 34 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.94489 Processing query 28 out of 34 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=1 Processing query 29 out of 34 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.997318 Processing query 30 out of 34 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=1 Processing query 31 out of 34 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.998089 Processing query 32 out of 34 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.976301 Processing query 33 out of 34 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.963545 Processing query 34 out of 34 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=1 Can't locate HtmlMonolithWr.pm: /root/lib/perl/HtmlMonolithWr.pm: Permission denied at /software/meme/4.11.2/bin/tomtom_xml_to_html line 48. Warning: tomtom_xml_to_html exited abnormally and may have failed to create HTML output.
Motif ID | q-val | PWM |
---|---|---|
MA0741.1-KLF16 | 0.00025475 | |
MA0685.2-SP4 | 0.00025475 | |
MA0742.2-KLF12 | 0.00025475 | |
MA0516.3-SP2 | 0.000261948 | |
MA1511.2-KLF10 | 0.000261948 |
Motif ID | q-val | PWM |
---|---|---|
MA0764.3-ETV4 | 4.47481e-05 | |
MA0076.2-ELK4 | 4.47481e-05 | |
MA0916.1-Ets21C | 4.71171e-05 | |
MA1854.1-Etv1/4/5 | 7.27157e-05 | |
MA0759.2-ELK3 | 0.000113081 |
Motif ID | q-val | PWM |
---|---|---|
MA0489.2-Jun | 7.75468e-05 | |
MA1988.1-Atf3 | 9.3236e-05 | |
MA1928.1-BNC2 | 9.3236e-05 | |
MA0591.1-Bach1::Mafk | 0.0003931 | |
MA0099.3-FOS::JUN | 0.0003931 |
Motif ID | q-val | PWM |
---|---|---|
MA0588.1-TGA1 | 0.00460754 | |
MA1129.1-FOSL1::JUN | 0.00460754 | |
MA0831.3-TFE3 | 0.00460754 | |
MA0609.2-CREM | 0.00460754 | |
MA1131.1-FOSL2::JUN | 0.00460754 |
Motif ID | q-val | PWM |
---|---|---|
MA0060.3-NFYA | 1.1169e-05 | |
MA1644.1-NFYC | 1.1169e-05 | |
MA0314.2-HAP3 | 1.1169e-05 | |
MA0502.2-NFYB | 0.0098343 | |
MA0316.1-HAP5 | 0.0103072 |
Motif ID | q-val | PWM |
---|---|---|
MA1651.1-ZFP42 | 0.00336629 | |
MA0748.2-YY2 | 0.00532593 | |
MA0095.3-Yy1 | 0.0451474 | |
MA1927.1-YY1-2 | 0.0451474 | |
MA1460.1-pho | 0.0757862 |
Motif ID | q-val | PWM |
---|---|---|
MA0833.2-ATF4 | 2.71858e-06 | |
MA1636.1-CEBPG | 9.13744e-05 | |
MA1702.1-Pdp1 | 0.0682883 | |
MA0025.2-NFIL3 | 0.0682883 | |
MA0488.1-JUN | 0.0912031 |
Motif ID | q-val | PWM |
---|---|---|
MA0506.2-Nrf1 | 0.000542228 | |
MA1412.1-TSAR2 | 0.462242 |
Motif ID | q-val | PWM |
---|---|---|
MA1034.1-Os05g0497200 | 0.00212664 | |
MA1818.1-Zm00001d052229 | 0.00212664 | |
MA1819.1-Zm00001d005892 | 0.00212664 | |
MA1832.1-Zm00001d002364 | 0.00212664 | |
MA0997.1-ERF069 | 0.00212664 |
Motif ID | q-val | PWM |
---|---|---|
MA0474.3-Erg | 2.28405e-06 | |
MA0062.3-GABPA | 2.28405e-06 | |
MA0473.3-ELF1 | 5.80906e-06 | |
MA0761.2-ETV1 | 5.80906e-06 | |
MA0598.3-EHF | 5.80906e-06 |
Motif ID | q-val | PWM |
---|---|---|
MA1573.2-Thap11 | 1.00021e-07 | |
MA0088.2-ZNF143 | 0.00794654 | |
MA1716.1-ZNF76 | 0.0161486 | |
MA1625.1-Stat5b | 0.115358 | |
MA0519.1-Stat5a::Stat5b | 0.168547 |
Motif ID | q-val | PWM |
---|---|---|
MA0506.2-Nrf1 | 0.0758358 |
Motif ID | q-val | PWM |
---|---|---|
MA0139.1-CTCF | 6.08737e-08 | |
MA1929.1-CTCF | 3.56838e-06 | |
MA1930.1-CTCF | 2.18475e-05 | |
MA1102.2-CTCFL | 2.18475e-05 | |
MA0531.1-CTCF | 3.12418e-05 |
Motif ID | q-val | PWM |
---|---|---|
MA0361.1-RDS1 | 0.0288135 | |
MA0429.1-YLL054C | 0.0288135 | |
MA0544.1-snpc-4 | 0.42518 |
Motif ID | q-val | PWM |
---|---|---|
MA0527.1-ZBTB33 | 1.68083e-07 |
Motif ID | q-val | PWM |
---|---|---|
MA0506.2-Nrf1 | 0.127445 | |
MA1817.1-Zm00001d020267 | 0.127445 | |
MA1826.1-bHLH145 | 0.127445 | |
MA1820.1-Zm00001d024324 | 0.127445 | |
MA0979.1-ERF008 | 0.127445 |
Motif ID | q-val | PWM |
---|---|---|
MA0506.2-Nrf1 | 0.0534958 | |
MA1650.1-ZBTB14 | 0.0534958 | |
MA1818.1-Zm00001d052229 | 0.0534958 | |
MA2022.1-LOB | 0.0534958 | |
MA1266.1-RAP2-11 | 0.0534958 |
Motif ID | q-val | PWM |
---|---|---|
MA1833.1-Zm00001d049364 | 0.00172652 | |
MA1817.1-Zm00001d020267 | 0.00589692 | |
MA1228.1-ERF091 | 0.00589692 | |
MA2013.1-ERF115 | 0.00910219 | |
MA1671.1-ERF118 | 0.00910219 |
Motif ID | q-val | PWM |
---|---|---|
MA0374.1-RSC3 | 0.03013 | |
MA1818.1-Zm00001d052229 | 0.0556004 | |
MA0531.1-CTCF | 0.0556004 | |
MA1832.1-Zm00001d002364 | 0.0556004 | |
MA1821.1-Zm00001d020595 | 0.0556004 |
Motif ID | q-val | PWM |
---|---|---|
MA1650.1-ZBTB14 | 0.242276 | |
MA0394.1-STP1 | 0.242276 | |
MA0399.1-SUT1 | 0.242276 | |
MA0320.1-IME1 | 0.242276 | |
MA1004.1-ERF13 | 0.242276 |
Motif ID | q-val | PWM |
---|---|---|
MA1833.1-Zm00001d049364 | 0.00266617 | |
MA1228.1-ERF091 | 0.00266617 | |
MA1053.1-ERF109 | 0.00266617 | |
MA1257.1-ERF9 | 0.00266617 | |
MA1262.1-ERF2 | 0.00266617 |
No TOMTOM matches passing threshold
Motif ID | q-val | PWM |
---|---|---|
MA0506.2-Nrf1 | 0.000474553 | |
MA1650.1-ZBTB14 | 0.00121867 | |
MA0374.1-RSC3 | 0.00495054 | |
MA1826.1-bHLH145 | 0.00701872 | |
MA0399.1-SUT1 | 0.0152841 |
Motif ID | q-val | PWM |
---|---|---|
MA1833.1-Zm00001d049364 | 0.00151446 | |
MA0506.2-Nrf1 | 0.00231364 | |
MA1239.1-ERF104 | 0.00231364 | |
MA2022.1-LOB | 0.00231364 | |
MA1246.1-LEP | 0.00231364 |
Motif ID | q-val | PWM |
---|---|---|
MA1006.1-ERF6 | 0.426275 | |
MA1728.1-ZNF549 | 0.426275 | |
MA1878.1-Hes-c | 0.426275 | |
MA1854.1-Etv1/4/5 | 0.426275 | |
MA0399.1-SUT1 | 0.426275 |
Motif ID | q-val | PWM |
---|---|---|
MA0836.2-CEBPD | 0.000339892 | |
MA0102.4-CEBPA | 0.00050521 | |
MA0837.2-CEBPE | 0.00292024 | |
MA0466.3-CEBPB | 0.00292024 | |
MA1702.1-Pdp1 | 0.00798822 |
Motif ID | q-val | PWM |
---|---|---|
MA1833.1-Zm00001d049364 | 5.30301e-06 | |
MA1817.1-Zm00001d020267 | 1.95309e-05 | |
MA1819.1-Zm00001d005892 | 1.95309e-05 | |
MA1820.1-Zm00001d024324 | 2.01619e-05 | |
MA2022.1-LOB | 5.0344e-05 |
Motif ID | q-val | PWM |
---|---|---|
MA1573.2-Thap11 | 5.14287e-05 | |
MA1687.1-ARF14 | 0.268811 |
Motif ID | q-val | PWM |
---|---|---|
MA0139.1-CTCF | 3.14561e-12 | |
MA1929.1-CTCF | 8.00842e-12 | |
MA1930.1-CTCF | 1.78251e-11 | |
MA1102.2-CTCFL | 0.00252869 | |
MA0531.1-CTCF | 0.00770196 |
No TOMTOM matches passing threshold
Motif ID | q-val | PWM |
---|---|---|
MA0798.3-RFX3 | 3.89302e-08 | |
MA0510.2-RFX5 | 3.89302e-08 | |
MA0509.3-RFX1 | 3.89302e-08 | |
MA0600.2-RFX2 | 3.89302e-08 | |
MA0365.1-RFX1 | 0.0318262 |
Motif ID | q-val | PWM |
---|---|---|
MA1573.2-Thap11 | 0.0520477 | |
MA1513.1-KLF15 | 0.0520477 | |
MA1716.1-ZNF76 | 0.065572 | |
MA1687.1-ARF14 | 0.065572 | |
MA1285.1-TCP9 | 0.065572 |
Motif ID | q-val | PWM |
---|---|---|
MA1513.1-KLF15 | 0.000201701 | |
MA0685.2-SP4 | 0.000317601 | |
MA0742.2-KLF12 | 0.000317601 | |
MA1511.2-KLF10 | 0.000317601 | |
MA1890.1-Klf15 | 0.000317601 |
Motif ID | q-val | PWM |
---|---|---|
MA0139.1-CTCF | 1.58201e-05 | |
MA1929.1-CTCF | 0.00385279 | |
MA0531.1-CTCF | 0.00385279 | |
MA1930.1-CTCF | 0.00385279 | |
MA1102.2-CTCFL | 0.0547218 |
The output directory '/users/kcochran//projects/procap_models/modisco_out/procap/bpnetlite_basic_v2/MCF10A/ENCSR799DGV/2022-07-05_09-52-52_run1_modisco/tomtom' already exists. Its contents will be overwritten. Processing query 1 out of 6 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.953111 Processing query 2 out of 6 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.948677 Processing query 3 out of 6 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=1 Processing query 4 out of 6 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=0.997318 Processing query 5 out of 6 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=1 Processing query 6 out of 6 Estimating pi_0 from all 3912 observed p-values. Estimating pi_0. Estimated pi_0=1 Can't locate HtmlMonolithWr.pm: /root/lib/perl/HtmlMonolithWr.pm: Permission denied at /software/meme/4.11.2/bin/tomtom_xml_to_html line 48. Warning: tomtom_xml_to_html exited abnormally and may have failed to create HTML output.
Motif ID | q-val | PWM |
---|---|---|
MA1890.1-Klf15 | 0.0050389 | |
MA1892.1-Klf5-like | 0.00678531 | |
MA1410.1-StBRC1 | 0.00678531 | |
MA1961.1-PATZ1 | 0.0114908 | |
MA1817.1-Zm00001d020267 | 0.0119187 |
Motif ID | q-val | PWM |
---|---|---|
MA1833.1-Zm00001d049364 | 0.0146857 | |
MA1712.1-ZNF454 | 0.0146857 | |
MA1880.1-Hey | 0.0146857 | |
MA1820.1-Zm00001d024324 | 0.0146857 | |
MA0163.1-PLAG1 | 0.0146857 |
No TOMTOM matches passing threshold
No TOMTOM matches passing threshold
No TOMTOM matches passing threshold
No TOMTOM matches passing threshold