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View Code? Open in Web Editor NEWConcise: Keras extension for regulatory genomics
Home Page: https://i12g-gagneurweb.in.tum.de/public/docs/concise/
License: MIT License
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stella-gao hhuang2018 s6juncheng zberlj muhammedhasan flesch91 shanring morphinggen houzl3416 harel-coffee dbogdanoconcise's Issues
Add activation and number of units to concise.layers.SplineT
Wrong Results using tpr, tnr, fpr, fnr
Hi,
I using the metrics (fpr, fnr, tpr, tnr) for my model in Keras (Tensorflow.python keras v2.1.2) as you can see:
model.compile(loss='categorical_crossentropy',
optimizer='adam',
metrics=['binary_accuracy', tpr, tnr, fpr, fnr])
But running this with history = model.fit_generator(..) am getting the accuracy on tpr and fpr; and 1-acc for tnr and fnr. For debugging I returned also the outputs of the contingency_table and tp=tn = all true predicitons and fp=fn = all false predicitons.
Do you have any suggestions how to fix this issue and get the right values? Thanks in advance!
Issue raised within concise while running `snakemake` in Manuscript_Avsec_Bioinformatics_2017
Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
count jobs
1 all
20 train_exclude_features
21
[Sat Dec 1 13:52:44 2018]
rule train_exclude_features:
input: data/eclip/processed/design_matrix/train/TBRG4_extended.csv, data/eclip/processed/design_matrix/valid/TBRG4_extended.csv, data/eclip/processed/design_matrix/test/TBRG4_extended.csv, Scripts/RBP/Eclip/predictive_models/train_exclude_features.py
output: data/eclip/processed/feature_exclusion_exp/results/TBRG4/DeepNN_scalar_position_ext_gam-excl-polya,gene_end.json
jobid: 26
wildcards: rbp_name=TBRG4, exp=DeepNN_scalar_position_ext_gam, fset=polya,gene_end
Using TensorFlow backend.
INFO:2018-12-01 13:52:57,891:excl_f] used_features: ['tss', 'exon_intron', 'intron_exon', 'start_codon', 'stop_codon', 'gene_start']
2018-12-01 13:52:57,891 [INFO] used_features: ['tss', 'exon_intron', 'intron_exon', 'start_codon', 'stop_codon', 'gene_start']
INFO:2018-12-01 13:52:57,891:excl_f] get the best hyper-parameters for a model
2018-12-01 13:52:57,891 [INFO] get the best hyper-parameters for a model
INFO:2018-12-01 13:52:57,892:excl_f] c_exp_name: DeepNN_scalar_position_ext_gam_TBRG4
2018-12-01 13:52:57,892 [INFO] c_exp_name: DeepNN_scalar_position_ext_gam_TBRG4
2018-12-01 13:52:57,892 [INFO] PROTOCOL mongo
2018-12-01 13:52:57,892 [INFO] USERNAME None
2018-12-01 13:52:57,892 [INFO] HOSTNAME localhost
2018-12-01 13:52:57,892 [INFO] PORT 27017
2018-12-01 13:52:57,892 [INFO] PATH /RBP__Eclip/jobs
2018-12-01 13:52:57,892 [INFO] AUTH DB None
2018-12-01 13:52:57,892 [INFO] DB RBP__Eclip
2018-12-01 13:52:57,892 [INFO] COLLECTION jobs
Traceback (most recent call last):
File "Scripts/RBP/Eclip/predictive_models/train_exclude_features.py", line 75, in <module>
tid = tr.best_trial_tid()
File "/home/cappelletti/code/.virtualenvs/virtual-py36gpu/lib/python3.6/site-packages/concise/hyopt.py", line 137, in best_trial_tid
lid = np.where(np.argsort(losses).argsort() == rank)[0][0]
IndexError: index 0 is out of bounds for axis 0 with size 0
[Sat Dec 1 13:52:58 2018]
Error in rule train_exclude_features:
jobid: 26
output: data/eclip/processed/feature_exclusion_exp/results/TBRG4/DeepNN_scalar_position_ext_gam-excl-polya,gene_end.json
RuleException:
CalledProcessError in line 123 of /data/Avsec/automated/Manuscript_Avsec_Bioinformatics_2017/Scripts/RBP/Eclip/Snakefile:
Command ' set -euo pipefail; python Scripts/RBP/Eclip/predictive_models/train_exclude_features.py --rbp=TBRG4 --feature_set=polya,gene_end --exp=DeepNN_scalar_position_ext_gam ' returned non-zero exit status 1.
File "/data/Avsec/automated/Manuscript_Avsec_Bioinformatics_2017/Scripts/RBP/Eclip/Snakefile", line 123, in __rule_train_exclude_features
File "/usr/local/lib/python3.6/concurrent/futures/thread.py", line 56, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /data/Avsec/automated/Manuscript_Avsec_Bioinformatics_2017/Scripts/RBP/Eclip/.snakemake/log/2018-12-01T135243.477113.snakemake.logPytest not passing
Hello, since trying to reproduce the other paper I had encountered exceptions from within this package I thought to test if everything was working correctly and I tried to run pytest. After installing the required packages, I have encountered the following errors:
MBP-di-Luca:concise-master lucacappelletti$ pytest
========================================================= test session starts =========================================================
platform darwin -- Python 3.6.6, pytest-3.3.2, py-1.5.2, pluggy-0.6.0
rootdir: /Users/lucacappelletti/Downloads/concise-master, inifile:
plugins: pep8-1.0.6, cov-2.5.1
collected 81 items
tests/test_GAMSmooth.py .. [ 2%]
tests/test_concise_keras.py ....... [ 11%]
tests/test_conv1d.py .. [ 13%]
tests/test_effects.py ....... [ 22%]
tests/test_eval.py . [ 23%]
tests/test_initializers.py ...... [ 30%]
tests/test_layers.py .....F... [ 41%]
tests/test_losses.py .. [ 44%]
tests/test_metrics.py ... [ 48%]
tests/data/test_attract.py . [ 49%]
tests/data/test_encode.py . [ 50%]
tests/data/test_hocomoco.py . [ 51%]
tests/layers/test_SplineT.py ............. [ 67%]
tests/preprocessing/test_sequence.py ..... [ 74%]
tests/preprocessing/test_splines.py ....... [ 82%]
tests/preprocessing/test_structure.py FFF [ 86%]
tests/utils/test_model_data.py ... [ 90%]
tests/utils/test_position.py .. [ 92%]
tests/utils/test_utils_pwm.py ...... [100%]
============================================================== FAILURES ===============================================================
_____________________________________ test_all_layers[seq3-encodeSEQ3-InputSEQ3-ConvRNAStructure] _____________________________________
seq = ['ACTTGAATA'], encodeSEQ = <function encodeRNAStructure at 0x1a1bb1d268>, InputSEQ = <function InputRNAStructure at 0x1a1c665378>
ConvSEQ = <class 'concise.layers.ConvRNAStructure'>
tmpdir = local('/private/var/folders/97/ljz_bpdd5qq6m3kxf6vdn0640000gn/T/pytest-of-lucacappelletti/pytest-0/test_all_layers_seq3_encodeSEQ0')
@pytest.mark.parametrize("seq, encodeSEQ, InputSEQ, ConvSEQ", [
(["ACTTGAATA"], encodeDNA, cl.InputDNA, cl.ConvDNA),
(["ACUUGAAUA"], encodeRNA, cl.InputRNA, cl.ConvRNA),
(["ACTTGAATA"], encodeCodon, cl.InputCodon, cl.ConvCodon),
(["ACTTGAATA"], encodeRNAStructure, cl.InputRNAStructure, cl.ConvRNAStructure),
(["ARNBCEQ"], encodeAA, cl.InputAA, cl.ConvAA),
(np.array([[1, 2, 3, 4, 5]]), encodeSplines, cl.InputSplines, cl.ConvSplines),
])
def test_all_layers(seq, encodeSEQ, InputSEQ, ConvSEQ, tmpdir):
seq_length = len(seq[0])
# pre-process
> train_x = encodeSEQ(seq)
tests/test_layers.py:70:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
concise/preprocessing/structure.py:134: in encodeRNAStructure
run_RNAplfold(fasta_path, tmpdir, W=W, L=L, U=U)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
input_fasta = '/tmp/RNAplfold//5158acaf-cb4f-49b2-a590-8771eae37917//input.fasta'
tmpdir = '/tmp/RNAplfold//5158acaf-cb4f-49b2-a590-8771eae37917/', W = 240, L = 160, U = 1
def run_RNAplfold(input_fasta, tmpdir, W=240, L=160, U=1):
"""
Arguments:
W, Int: span - window length
L, Int, maxiumm span
U, Int, size of unpaired region
"""
profiles = RNAplfold_PROFILES_EXECUTE
for i, P in enumerate(profiles):
print("running {P}_RNAplfold... ({i}/{N})".format(P=P, i=i + 1, N=len(profiles)))
command = "{bin}/{P}_RNAplfold".format(bin=RNAplfold_BIN_DIR, P=P)
file_out = "{tmp}/{P}_profile.fa".format(tmp=tmpdir, P=P)
args = " -W {W} -L {L} -u {U} < {fa} > {file_out}".format(W=W, L=L, U=U, fa=input_fasta, file_out=file_out)
os.system(command + args)
# check if the file is empty
if os.path.getsize(file_out) == 0:
> raise Exception("command wrote an empty file: {0}".format(file_out))
E Exception: command wrote an empty file: /tmp/RNAplfold//5158acaf-cb4f-49b2-a590-8771eae37917//H_profile.fa
concise/preprocessing/structure.py:38: Exception
-------------------------------------------------------- Captured stdout call ---------------------------------------------------------
running H_RNAplfold... (1/4)
-------------------------------------------------------- Captured stderr call ---------------------------------------------------------
sh: /Users/lucacappelletti/Downloads/concise-master/concise/resources/RNAplfold/H_RNAplfold: cannot execute binary file
_______________________________________________________ test_encodeRNAstructure _______________________________________________________
def test_encodeRNAstructure():
with cd("/tmp/"):
# what we want: seqs, values, chanells?
seq = ["TATTATGTATATGTATA", "TATGTATAT"]
> arr = encodeRNAStructure(seq)
tests/preprocessing/test_structure.py:38:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
concise/preprocessing/structure.py:134: in encodeRNAStructure
run_RNAplfold(fasta_path, tmpdir, W=W, L=L, U=U)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
input_fasta = '/tmp/RNAplfold//6e620cf5-fe37-46f7-9959-11407f171fdf//input.fasta'
tmpdir = '/tmp/RNAplfold//6e620cf5-fe37-46f7-9959-11407f171fdf/', W = 240, L = 160, U = 1
def run_RNAplfold(input_fasta, tmpdir, W=240, L=160, U=1):
"""
Arguments:
W, Int: span - window length
L, Int, maxiumm span
U, Int, size of unpaired region
"""
profiles = RNAplfold_PROFILES_EXECUTE
for i, P in enumerate(profiles):
print("running {P}_RNAplfold... ({i}/{N})".format(P=P, i=i + 1, N=len(profiles)))
command = "{bin}/{P}_RNAplfold".format(bin=RNAplfold_BIN_DIR, P=P)
file_out = "{tmp}/{P}_profile.fa".format(tmp=tmpdir, P=P)
args = " -W {W} -L {L} -u {U} < {fa} > {file_out}".format(W=W, L=L, U=U, fa=input_fasta, file_out=file_out)
os.system(command + args)
# check if the file is empty
if os.path.getsize(file_out) == 0:
> raise Exception("command wrote an empty file: {0}".format(file_out))
E Exception: command wrote an empty file: /tmp/RNAplfold//6e620cf5-fe37-46f7-9959-11407f171fdf//H_profile.fa
concise/preprocessing/structure.py:38: Exception
-------------------------------------------------------- Captured stdout call ---------------------------------------------------------
running H_RNAplfold... (1/4)
-------------------------------------------------------- Captured stderr call ---------------------------------------------------------
sh: /Users/lucacappelletti/Downloads/concise-master/concise/resources/RNAplfold/H_RNAplfold: cannot execute binary file
_________________________________________________________ test_other_objects __________________________________________________________
def test_other_objects():
seq = np.array(["TATTATGTATATGTATA", "TATGTATAT"])
> arr = encodeRNAStructure(seq)
tests/preprocessing/test_structure.py:46:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
concise/preprocessing/structure.py:134: in encodeRNAStructure
run_RNAplfold(fasta_path, tmpdir, W=W, L=L, U=U)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
input_fasta = '/tmp/RNAplfold//2035953c-fd3f-4c12-b76a-0fe72b0658a5//input.fasta'
tmpdir = '/tmp/RNAplfold//2035953c-fd3f-4c12-b76a-0fe72b0658a5/', W = 240, L = 160, U = 1
def run_RNAplfold(input_fasta, tmpdir, W=240, L=160, U=1):
"""
Arguments:
W, Int: span - window length
L, Int, maxiumm span
U, Int, size of unpaired region
"""
profiles = RNAplfold_PROFILES_EXECUTE
for i, P in enumerate(profiles):
print("running {P}_RNAplfold... ({i}/{N})".format(P=P, i=i + 1, N=len(profiles)))
command = "{bin}/{P}_RNAplfold".format(bin=RNAplfold_BIN_DIR, P=P)
file_out = "{tmp}/{P}_profile.fa".format(tmp=tmpdir, P=P)
args = " -W {W} -L {L} -u {U} < {fa} > {file_out}".format(W=W, L=L, U=U, fa=input_fasta, file_out=file_out)
os.system(command + args)
# check if the file is empty
if os.path.getsize(file_out) == 0:
> raise Exception("command wrote an empty file: {0}".format(file_out))
E Exception: command wrote an empty file: /tmp/RNAplfold//2035953c-fd3f-4c12-b76a-0fe72b0658a5//H_profile.fa
concise/preprocessing/structure.py:38: Exception
-------------------------------------------------------- Captured stdout call ---------------------------------------------------------
running H_RNAplfold... (1/4)
-------------------------------------------------------- Captured stderr call ---------------------------------------------------------
sh: /Users/lucacappelletti/Downloads/concise-master/concise/resources/RNAplfold/H_RNAplfold: cannot execute binary file
___________________________________________________________ test_real_data ____________________________________________________________
def test_real_data():
csv_file_path = "data/pombe_half-life_UTR3.csv"
dt = pd.read_csv(csv_file_path)
seq_vec = dt["seq"][:6]
> a = encodeRNAStructure(seq_vec)
tests/preprocessing/test_structure.py:55:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
concise/preprocessing/structure.py:134: in encodeRNAStructure
run_RNAplfold(fasta_path, tmpdir, W=W, L=L, U=U)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
input_fasta = '/tmp/RNAplfold//4c0c20c2-ca9f-45a0-b2e7-a5933a2528b1//input.fasta'
tmpdir = '/tmp/RNAplfold//4c0c20c2-ca9f-45a0-b2e7-a5933a2528b1/', W = 240, L = 160, U = 1
def run_RNAplfold(input_fasta, tmpdir, W=240, L=160, U=1):
"""
Arguments:
W, Int: span - window length
L, Int, maxiumm span
U, Int, size of unpaired region
"""
profiles = RNAplfold_PROFILES_EXECUTE
for i, P in enumerate(profiles):
print("running {P}_RNAplfold... ({i}/{N})".format(P=P, i=i + 1, N=len(profiles)))
command = "{bin}/{P}_RNAplfold".format(bin=RNAplfold_BIN_DIR, P=P)
file_out = "{tmp}/{P}_profile.fa".format(tmp=tmpdir, P=P)
args = " -W {W} -L {L} -u {U} < {fa} > {file_out}".format(W=W, L=L, U=U, fa=input_fasta, file_out=file_out)
os.system(command + args)
# check if the file is empty
if os.path.getsize(file_out) == 0:
> raise Exception("command wrote an empty file: {0}".format(file_out))
E Exception: command wrote an empty file: /tmp/RNAplfold//4c0c20c2-ca9f-45a0-b2e7-a5933a2528b1//H_profile.fa
concise/preprocessing/structure.py:38: Exception
-------------------------------------------------------- Captured stdout call ---------------------------------------------------------
running H_RNAplfold... (1/4)
-------------------------------------------------------- Captured stderr call ---------------------------------------------------------
sh: /Users/lucacappelletti/Downloads/concise-master/concise/resources/RNAplfold/H_RNAplfold: cannot execute binary file
========================================================== warnings summary ===========================================================
tests/test_effects.py::test_dropout
/anaconda3/lib/python3.6/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
return (self.a < x) & (x < self.b)
/anaconda3/lib/python3.6/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
return (self.a < x) & (x < self.b)
/anaconda3/lib/python3.6/site-packages/scipy/stats/_distn_infrastructure.py:1821: RuntimeWarning: invalid value encountered in less_equal
cond2 = cond0 & (x <= self.a)
/Users/lucacappelletti/Downloads/concise-master/concise/effects/dropout.py:250: RuntimeWarning: invalid value encountered in greater
sel = (np.abs(prob) > np.abs(prob_rc)).astype(np.int) # Select the LOWER p-value among fwd and rc
/anaconda3/lib/python3.6/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
return (self.a < x) & (x < self.b)
/anaconda3/lib/python3.6/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
return (self.a < x) & (x < self.b)
/anaconda3/lib/python3.6/site-packages/scipy/stats/_distn_infrastructure.py:1821: RuntimeWarning: invalid value encountered in less_equal
cond2 = cond0 & (x <= self.a)
/Users/lucacappelletti/Downloads/concise-master/concise/effects/dropout.py:250: RuntimeWarning: invalid value encountered in greater
sel = (np.abs(prob) > np.abs(prob_rc)).astype(np.int) # Select the LOWER p-value among fwd and rc
tests/test_effects.py::test_ism
/Users/lucacappelletti/Downloads/concise-master/concise/effects/ism.py:69: UserWarning: Using log_odds on model outputs that are not bound [0,1]
warnings.warn("Using log_odds on model outputs that are not bound [0,1]")
/Users/lucacappelletti/Downloads/concise-master/concise/effects/ism.py:70: RuntimeWarning: invalid value encountered in log
diffs = np.log(preds["alt"] / (1 - preds["alt"])) - np.log(preds["ref"] / (1 - preds["ref"]))
/Users/lucacappelletti/Downloads/concise-master/concise/effects/ism.py:71: RuntimeWarning: invalid value encountered in log
diffs_rc = np.log(preds["alt_rc"] / (1 - preds["alt_rc"])) - np.log(preds["ref_rc"] / (1 - preds["ref_rc"]))
/Users/lucacappelletti/Downloads/concise-master/concise/effects/ism.py:79: RuntimeWarning: invalid value encountered in less
replace_filt = np.abs(diffs) < np.abs(diffs_rc)
tests/test_effects.py::test_effect_from_model
/anaconda3/lib/python3.6/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in greater
return (self.a < x) & (x < self.b)
/anaconda3/lib/python3.6/site-packages/scipy/stats/_distn_infrastructure.py:879: RuntimeWarning: invalid value encountered in less
return (self.a < x) & (x < self.b)
/anaconda3/lib/python3.6/site-packages/scipy/stats/_distn_infrastructure.py:1821: RuntimeWarning: invalid value encountered in less_equal
cond2 = cond0 & (x <= self.a)
/Users/lucacappelletti/Downloads/concise-master/concise/effects/dropout.py:250: RuntimeWarning: invalid value encountered in greater
sel = (np.abs(prob) > np.abs(prob_rc)).astype(np.int) # Select the LOWER p-value among fwd and rc
/Users/lucacappelletti/Downloads/concise-master/concise/effects/ism.py:69: UserWarning: Using log_odds on model outputs that are not bound [0,1]
warnings.warn("Using log_odds on model outputs that are not bound [0,1]")
/Users/lucacappelletti/Downloads/concise-master/concise/effects/ism.py:70: RuntimeWarning: invalid value encountered in log
diffs = np.log(preds["alt"] / (1 - preds["alt"])) - np.log(preds["ref"] / (1 - preds["ref"]))
/Users/lucacappelletti/Downloads/concise-master/concise/effects/ism.py:71: RuntimeWarning: invalid value encountered in log
diffs_rc = np.log(preds["alt_rc"] / (1 - preds["alt_rc"])) - np.log(preds["ref_rc"] / (1 - preds["ref_rc"]))
/Users/lucacappelletti/Downloads/concise-master/concise/effects/ism.py:79: RuntimeWarning: invalid value encountered in less
replace_filt = np.abs(diffs) < np.abs(diffs_rc)
-- Docs: http://doc.pytest.org/en/latest/warnings.html
========================================= 4 failed, 77 passed, 20 warnings in 536.29 seconds ==========================================Add Cyclic LR callback
Upgrade to latest Tensorflow + Keras
Should be done soon.
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