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example.log.txt
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>> python promotech.py -s -m RF-HOT -f examples/sequences/test.fasta
PROMOTECH
MODE : COMMAND-LINE
ML MODEL : FASTA FILE
INPUT TYPE : RF-HOT
INPUT : ['examples/sequences/test.fasta']
TEST SAMPLES : None
READING FASTA FILE: examples/sequences/test.fasta
SAMPLE:
{'id': 'NC_000913.2:2541-2581(+)|POSITIVE', 'seq': 'GCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAATA'}
# SEQS: 9. SAMPLE: GCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAATA
TIME ELAPSED FROM START (HOUR:MIN:SEC): 00:00:00
CONVERTING SEQUENCES TO RF-HOT DATA TYPE
INPUT SHAPE 9
SAMPLE WITH LEN 40:
GCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAATA
CONVERTING DATA
N/A% (0 of 9) | | Elapsed Time: 0:00:00 ETA: --:--:--
HOT ENCODED SEQUENCES GENERATED SUCCESSFULLY.
A G C T A ... T A G C T
0 0 1 0 0 0 ... 1 1 0 0 0
1 1 0 0 0 1 ... 1 0 0 0 1
2 1 0 0 0 0 ... 1 1 0 0 0
3 0 0 1 0 0 ... 0 1 0 0 0
4 0 1 0 0 1 ... 0 1 0 0 0
[5 rows x 160 columns]
TIME ELAPSED FROM START (HOUR:MIN:SEC): 00:00:00
LOADING ML MODEL models/RF-HOT.model
/home/ruben/miniconda3/envs/promotech_env/lib/python3.6/site-packages/sklearn/base.py:334: UserWarning: Trying to unpickle estimator DecisionTreeClassifier from version 0.23.0 when using version 0.23.1. This might lead to breaking code or invalid results. Use at your own risk.
UserWarning)
/home/ruben/miniconda3/envs/promotech_env/lib/python3.6/site-packages/sklearn/base.py:334: UserWarning: Trying to unpickle estimator RandomForestClassifier from version 0.23.0 when using version 0.23.1. This might lead to breaking code or invalid results. Use at your own risk.
UserWarning)
/home/ruben/miniconda3/envs/promotech_env/lib/python3.6/site-packages/sklearn/base.py:334: UserWarning: Trying to unpickle estimator GridSearchCV from version 0.23.0 when using version 0.23.1. This might lead to breaking code or invalid results. Use at your own risk.
UserWarning)
TIME ELAPSED FROM START (HOUR:MIN:SEC): 00:00:12
PREDICTING SEQUNCES USING:
GridSearchCV(cv=10,
estimator=RandomForestClassifier(class_weight={0: 0.5512173740112261,
1: 5.381156147232458},
min_samples_leaf=5, verbose=2),
iid=False,
param_grid={'max_features': ['log2'], 'n_estimators': [2000]},
refit='average_precision',
scoring=['average_precision', 'precision', 'recall'], verbose=2)
[Parallel(n_jobs=1)]: Using backend SequentialBackend with 1 concurrent workers.
[Parallel(n_jobs=1)]: Done 1 out of 1 | elapsed: 0.0s remaining: 0.0s
[Parallel(n_jobs=1)]: Done 2000 out of 2000 | elapsed: 0.1s finished
PREDICTIONS GENERATED SUCCESSFULLY. SAMPLE:
CHROM PRED SEQ
0 NC_000913.2:2541-2581(+)|POSITIVE 0.832246 GCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAATA
1 NC_000913.2:5107-5147(+)|POSITIVE 0.713419 AAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATT
2 NC_000913.2:8002-8042(+)|POSITIVE 0.642305 ACGTTACCAATTGTTTAAGAAGTATATACGCTACGAGGTA
3 NC_000913.2:8052-8092(-)|POSITIVE 0.735783 CCCGCCATTTTTATACAAAACCTCATGTATGCTACGCAGA
4 NC_000913.2:2315833-2315873(+)|NEGATIVE 0.095024 GAATACGCACGGTAAACTGGCTGCCCATTCCCGGTTCTGA.
SAVED AT results/sequences_predictions.csv
TIME ELAPSED FROM START (HOUR:MIN:SEC): 00:00:12