predict a new pair #1
Description
@NWPU-903PR
Hi!
I just used LPI-BLS to predict a new pair following readme, but I get wrong. What's more, I have done 5 fold cross-validation successfully.
(py37) [ymwang @ ~/linqin/SourceCode/LPI_BLS]$ tail nohup.out
---5 run BLS5---
0.8144329896907216 0.875 0.7551020408163265 0.6341594043154593
---6 run stacked ensemble ---
0.9072164948453608 0.9166666666666666 0.8979591836734694 0.814625850340136
BLS1--- acc--- 0.7603829160530191 sn--- 0.7123299319727892 sp--- 0.8081632653061224 mcc--- 0.5284803311987807
BLS2--- acc--- 0.8832526825163056 sn--- 0.8314625850340136 sp--- 0.9346938775510203 mcc--- 0.7717422815089279
BLS3--- acc--- 0.8934567641489586 sn--- 0.8438775510204082 sp--- 0.9428571428571428 mcc--- 0.7933650289042681
BLS4--- acc--- 0.7520302966547444 sn--- 0.7573979591836735 sp--- 0.7469387755102042 mcc--- 0.5060723558169202
BLS5--- acc--- 0.7869556069850621 sn--- 0.7738945578231292 sp--- 0.8 mcc--- 0.5768774397176644
stacked ensemble --- acc--- 0.8934567641489586 sn--- 0.8479591836734695 sp--- 0.9387755102040817 mcc--- 0.7922312889652525
(py37) [ymwang @ ~/linqin/SourceCode/LPI_BLS]$
#pse feature predict
(py37) [ymwang @ ~/linqin/SourceCode/LPI_BLS]$ cat Pse-in-One-1.0.5/Pse-in-One
Pse-in-One/ Pse-in-One_manual.pdf
(py37) [ymwang @ ~/linqin/SourceCode/LPI_BLS]$ cat Pse-in-One-1.0.5/Pse-in-One/shuf5_pse.sh
#pse feature
for line in $(cat /home2/ymwang/linqin/SourceCode/LPI_BLS/gse112055/shuf5_lncrna1)
do
python pse.py /home2/ymwang/linqin/SourceCode/LPI_BLS/gse112055/shuf5/$line $line"_pse_feature" RNA PC-PseDNC-General -lamada=6 -w=0.9
mv $line"_pse_feature" /home2/ymwang/linqin/SourceCode/LPI_BLS/gse112055/pse_out/
done
for line in $(cat /home2/ymwang/linqin/SourceCode/LPI_BLS/gse112055/shuf5_protein1)
do
python pse.py /home2/ymwang/linqin/SourceCode/LPI_BLS/gse112055/shuf5/$line $line"_pse_feature" Protein PC-PseAAC-General -lamada=9 -w=0.5
mv $line"_pse_feature" /home2/ymwang/linqin/SourceCode/LPI_BLS/gse112055/pse_out/
done
(py37) [ymwang @ ~/linqin/SourceCode/LPI_BLS]$ python LPI_BLS.py -pair ENSMUST00000224375-Q8JZS2 -rf gse112055/shuf5/ENSMUST00000224375 -pf gse112055/shuf5/Q8JZS2 -rP gse112055/pse_out/ENSMUST00000224375_pse_feature -pP gse112055/pse_out/Q8JZS2_pse_feature
---------get kmer feature---------------
---------get ktuple feature---------------
---predicting---
Traceback (most recent call last):
File "LPI_BLS.py", line 466, in <module>
LPI_BL_new(pairs_file, lncRNA_fa, protein_fa, lncRNA_pse, protein_pse)
File "LPI_BLS.py", line 350, in LPI_BL_new
x_test_1, x_test_2, x_test_3, x_test_4, x_test_5, y_test, N1, N2, N3)
File "LPI_BLS.py", line 305, in run_stacking
test_prob_cv_1 = BroadLearningSystem.BLS(xx_train1, yy_train, x_test_cv1, y_test_cv, 1, 10**-10, N1, N2, N3)
File "/home2/ymwang/linqin/SourceCode/LPI_BLS/BroadLearningSystem.py", line 138, in BLS
test_x = preprocessing.scale(test_x,axis = 1)#,with_mean = True,with_std = True) #处理数据 x = (x-mean(x))/std(x) x属于[-1，1]
File "/home2/ymwang/miniconda3/envs/py37/lib/python3.7/site-packages/sklearn/utils/validation.py", line 73, in inner_f
return f(**kwargs)
File "/home2/ymwang/miniconda3/envs/py37/lib/python3.7/site-packages/sklearn/preprocessing/_data.py", line 143, in scale
force_all_finite='allow-nan')
File "/home2/ymwang/miniconda3/envs/py37/lib/python3.7/site-packages/sklearn/utils/validation.py", line 73, in inner_f
return f(**kwargs)
File "/home2/ymwang/miniconda3/envs/py37/lib/python3.7/site-packages/sklearn/utils/validation.py", line 654, in check_array
context))
ValueError: Found array with 0 sample(s) (shape=(0, 599)) while a minimum of 1 is required by the scale function.
(py37) [ymwang @ ~/linqin/SourceCode/LPI_BLS]$ cat gse112055/shuf5/ENSMUST00000224375 gse112055/shuf5/Q8JZS2
>ENSMUST00000224375.1
AGUGUCACUGGAGGGAGACUGUGCAGACUUCAAGAGCAUAGCCAAGGAGAGGAUGGUUUUGAUCUACUGCCUGAAGACAUGCUGUGUCACCACCAGAGCCCAAACAACUGGACAGAGCCAGCACCAACCAAAACCUACAAAGCUAUCUGGUUUAUCCCUUCCCAGAAGACAAACUGCAACCAGAUGAAGGCCUUAUUGUCAUCCAAACUUGCCUGGAACUAGUUAAGGAUAAACGGACUCUCCUGUCUGUACCGCUGUAUGUCACCACUGUGUGUCACCACACCCAAGCUUACUUAGUGCUGGAGAUUAGUCCACUGCUUUCUGUCUGCCAGGCAAACUUUCUACUCCCUCAGGAACAUCCACAGCCACAACUACAAAAUUGUGUUCAUUGUGAGUCAAGUACUCUGUAUAUAUAGUCAUCAUUCUUCCGGUCCAAGAUCACCUAAAGUUGUCAUCUUUUUUUUUUUUCAAUUGAGAAUACAUUGGUGGAAAACACCCAGUUUCAGAUUUUUGUGAUGGGAAACGUUGUCAUCUCAAGAGGAAAUUCUCAGUCACAUGUAGAUUGCCUUGGAAAAAUAGAUUCCACUAAAUAUCUUUACAUUAUUUAAAUGAUGUUGUUUGUAUAAGUACAUUUAUAAUGUUCACUAUUUUCUGUAACUUGGGGAAAUGAGGCAUAGAAAGACAAAAAGCAGAGAGGCAAGGCUACAAAAGGUUGAGAGACUGAAGAAAGGGUCUGCAAGCUGGAAAAUCGAUAACUAGCUGCUAUUUAUUUCUCCCCAAAGCCCAUUUUAUUGCAAAGCAAUUUUUAAUCUGUAUUUGACCUAAAGACCAGUGAAGGAAGAAGAAAAAUACUUUUUCUUCAGUUACAUUAGGGCUACCUCAAUUGUGUUUAAUUCCAACAUACAAUUUCAAUUUUGAGAUUUACCAAGUGGGAUUCCUAGGGUAGAGAUUGAUGGUCAUUUGGCCUCUUUUCUCAGUGGUUCAGUUGGUUUUGCAGAAAACAAGGACUCUUGUUUGAUUUUCACUGUGCCCCAUGGAUCAACUCCAUUUCCAUAAUUGAAUAUUACAGUAUGGGUAUGUCUCUUCACCCCCACAGGUGUGUGCAUGUGAUUCUCUGCAACACCCACAUGACAUCACCAACCUGUUUGACUAUAAAAACCCUGGAUGCCUUCCUGGGCAAAGUAUUGAUCGUGAAUAGCAGAGAAAUUAAAUUUGUAUCUUUAUCAUAUUAAAUCUAGAUGAAAUUAUAUCAUCUGUUGUUCUGUAUUAUAAAUUCUGAGUGUUUGUACAUUGAUCAUGCUGAGAAUUAUACUUUGAAAUUGGGUAGAAAAGUCCUUAAUGAUUUUUUUUUUGUGACAUGUUGGUAAUUAAAUAGUGAGAAAAAUAAUUCCUGGACUUGAAAAGCAAGGUAGCAAAUGAAGGUUUUAUGCACAAAAUAAUAUCCUGUCACCUUCUGCUUAAACAGCACAAAUAUCUGUGGAGCUACAAAGGCUUAUCAGUACAUUUUAAAUGUUUGAUUAUUUACAGAUAUUGAAUAUCUCAGCUGUUUCAAAAGAACAAAACAGUUAACAAAAAUGUGUUCAUUACUUAGCUAGGAAAUAAAAUAAUUAGAAUAUAAUG
>Q8JZS2
MFRMLSSSFEDDPFFADSFLAHRESMRNMMRSFSEPLGRDLLSISDGRGRTHNRRERDDGEDSLTATSFSLVPFGRFGGMHADVNPFQTMDRMMANMRSGIQELQRNFGQLSMDPNGHSFCSSSVMTYSKVGDEPPKVFQASTQTRRAPGGVKETRKAMRDSDSGLERMAVGHHIHDRGHVIRKSKNNKTGDEEVNQEFINMNESDAHAFDDEWQNEVLKYKSIGRSGNTGMRSVGHEHPGSRELKRREKIHRNSAIESGRRSNVFVDKLNVKGSPVKITKK
(py37) [ymwang @ ~/linqin/SourceCode/LPI_BLS]$ cat gse112055/pse_out/ENSMUST00000224375_pse_feature
0.010198 0.00515629 0.00601567 0.00790631 0.00721881 0.00401045 0.00034375 0.00572921 0.00561463 0.00286461 0.00343753 0.00521358 0.00618755 0.00527087 0.00739068 0.010198 0.17514394 0.1494884 0.14378784 0.14426424 0.14781217 0.14674749
(py37) [ymwang @ ~/linqin/SourceCode/LPI_BLS]$ cat gse112055/pse_out/Q8JZS2_pse_feature
0.0040726 0.00033938 0.00678766 0.00644828 0.00543013 0.0081452 0.0040726 0.00305445 0.00543013 0.00441198 0.00543013 0.00543013 0.00339383 0.00271507 0.00984211 0.01086026 0.00373322 0.00509075 0.00033938 0.00067877 0.09767105 0.11047165 0.10214326 0.09386407 0.09835324 0.10276572 0.09029862 0.10729729 0.10142905
(py37) [ymwang @ ~/linqin/SourceCode/LPI_BLS]$ ll
total 60
drwxrwxr-x 7 ymwang ymwang 4096 Jun 24 17:34 ./
drwxrwxr-x 20 ymwang ymwang 4096 Jun 24 14:52 ../
-rw-rw-r-- 1 ymwang ymwang 6223 Jun 24 13:31 BroadLearningSystem.py
drwxrwxr-x 2 ymwang ymwang 4096 Jun 24 13:31 data/
-rw-rw-r-- 1 ymwang ymwang 0 Jun 24 17:34 ENSMUST00000224375-Q8JZS2
drwxrwxr-x 8 ymwang ymwang 4096 Jun 24 13:31 .git/
drwxrwxr-x 4 ymwang ymwang 4096 Jun 24 16:12 gse112055/
-rw-rw-r-- 1 ymwang ymwang 20144 Jun 24 13:31 LPI_BLS.py
-rw------- 1 ymwang ymwang 3481 Jun 24 15:10 nohup.out
-rw-rw-r-- 1 ymwang ymwang 1378 Jun 24 17:27 predict_shuf5.sh
drwxrwxr-x 3 ymwang ymwang 119 Jun 24 13:31 Pse-in-One-1.0.5/
drwxrwxr-x 2 ymwang ymwang 55 Jun 24 14:30 __pycache__/
-rw-rw-r-- 1 ymwang ymwang 1102 Jun 24 13:31 README.md
(py37) [ymwang @ ~/linqin/SourceCode/LPI_BLS]$
What's the problem?
Best,
Ci