Merge pull request #22 from Goosang-Yu/develop

🔖 Release v0.8.1
Goosang-Yu · Aug 9, 2023 · 7781bac · 7781bac
2 parents 3eb1e1c + 30a376b
commit 7781bac
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diff --git a/README.md b/README.md
@@ -95,11 +95,11 @@ df_out = spcas.predict(list_target)
 
 >>> df_out
 ```
-|   | Sequence                       | SpCas9   |
-| - | ------------------------------ | -------- |
-| 0 | TCACCTTCGTTTTTTTCCTTCTGCAGGAGG | 2.801168 |
-| 1 | CCTTCGTTTTTTTCCTTCTGCAGGAGGACA | 2.253283 |
-| 2 | CTTTCAAGAACTCTTCCACCTCCATGGTGT | 53.43183 |
+|        | Target                         | Spacer               | SpCas9   |
+| ------ | ------------------------------ | -------------------- | -------- |
+| 0      | TCACCTTCGTTTTTTTCCTTCTGCAGGAGG | CTTCGTTTTTTTCCTTCTGC | 2.801172 |
+| 1      | CCTTCGTTTTTTTCCTTCTGCAGGAGGACA | CGTTTTTTTCCTTCTGCAGG | 2.253288 |
+| 2      | CTTTCAAGAACTCTTCCACCTCCATGGTGT | CAAGAACTCTTCCACCTCCA | 53.43182 |
 
 
 ## Tutorial 2: Predict SpCas9variants activity (by DeepSpCas9variants)
@@ -125,11 +125,11 @@ df_out = cas_ng.predict(list_target30)
 
 >>> df_out
 ```
-|   | Sequence                       | SpCas9-NG |
-| - | ------------------------------ | --------- |
-| 0 | TCACCTTCGTTTTTTTCCTTCTGCAGGAGG | 0.618299  |
-| 1 | CCTTCGTTTTTTTCCTTCTGCAGGAGGACA | 1.134845  |
-| 2 | CTTTCAAGAACTCTTCCACCTCCATGGTGT | 36.74358  |
+|   | Target                         | Spacer               | SpCas9-NG |
+| - | ------------------------------ | -------------------- | --------- |
+| 0 | TCACCTTCGTTTTTTTCCTTCTGCAGGAGG | CTTCGTTTTTTTCCTTCTGC | 0.618299  |
+| 1 | CCTTCGTTTTTTTCCTTCTGCAGGAGGACA | CGTTTTTTTCCTTCTGCAGG | 1.134845  |
+| 2 | CTTTCAAGAACTCTTCCACCTCCATGGTGT | CAAGAACTCTTCCACCTCCA | 36.74358  |
 
 ## Tutorial 3: Predict Prime editing efficiency (by DeepPrime and DeepPrime-FT)
 ![](docs/images/Fig3_DeepPrime_architecture.svg)
@@ -149,26 +149,33 @@ alt_type = 'sub1'
 df_pe = prd.pe_score(seq_wt, seq_ed, alt_type)
 df_pe.head()
 ```
-output:
-|    | ID     | WT74_On                                                                    | Edited74_On                                                                |   PBSlen |   RTlen |   RT-PBSlen |   Edit_pos |   Edit_len |   RHA_len |   type_sub |   type_ins |   type_del |     Tm1 |     Tm2 |   Tm2new |      Tm3 |     Tm4 |      TmD |   nGCcnt1 |   nGCcnt2 |   nGCcnt3 |   fGCcont1 |   fGCcont2 |   fGCcont3 |   MFE3 |   MFE4 |   DeepSpCas9_score |   PE2max_score |
-|---:|:-------|:---------------------------------------------------------------------------|:---------------------------------------------------------------------------|---------:|--------:|------------:|-----------:|-----------:|----------:|-----------:|-----------:|-----------:|--------:|--------:|---------:|---------:|--------:|---------:|----------:|----------:|----------:|-----------:|-----------:|-----------:|-------:|-------:|-------------------:|------------------:|
-|  0 | Sample | ATAAAAGACAACACCCTTGCCTTGTGGAGTTTTCAAAGCTCCCAGAAACTGAGAAGAACTATAACCTGCAAATG | xxxxxxxxxxxxxxCCTTGCCTTGTGGAGTTTTCAAAGCTCCCAGAAACTGAGACGxxxxxxxxxxxxxxxxxx |        7 |      35 |          42 |         34 |          1 |         1 |          1 |          0 |          0 | 16.191  | 62.1654 |  62.1654 | -277.939 | 58.2253 | -340.105 |         5 |        16 |        21 |    71.4286 |    45.7143 |    50      |  -10.4 |   -0.6 |            45.9675 |         0.0202249 |
-|  1 | Sample | ATAAAAGACAACACCCTTGCCTTGTGGAGTTTTCAAAGCTCCCAGAAACTGAGAAGAACTATAACCTGCAAATG | xxxxxxxxxxxxxCCCTTGCCTTGTGGAGTTTTCAAAGCTCCCAGAAACTGAGACGxxxxxxxxxxxxxxxxxx |        8 |      35 |          43 |         34 |          1 |         1 |          1 |          0 |          0 | 30.1995 | 62.1654 |  62.1654 | -277.939 | 58.2253 | -340.105 |         6 |        16 |        22 |    75      |    45.7143 |    51.1628 |  -10.4 |   -0.6 |            45.9675 |         0.0541608 |
-|  2 | Sample | ATAAAAGACAACACCCTTGCCTTGTGGAGTTTTCAAAGCTCCCAGAAACTGAGAAGAACTATAACCTGCAAATG | xxxxxxxxxxxxACCCTTGCCTTGTGGAGTTTTCAAAGCTCCCAGAAACTGAGACGxxxxxxxxxxxxxxxxxx |        9 |      35 |          44 |         34 |          1 |         1 |          1 |          0 |          0 | 33.7839 | 62.1654 |  62.1654 | -277.939 | 58.2253 | -340.105 |         6 |        16 |        22 |    66.6667 |    45.7143 |    50      |  -10.4 |   -0.6 |            45.9675 |         0.051455  |
-|  3 | Sample | ATAAAAGACAACACCCTTGCCTTGTGGAGTTTTCAAAGCTCCCAGAAACTGAGAAGAACTATAACCTGCAAATG | xxxxxxxxxxxCACCCTTGCCTTGTGGAGTTTTCAAAGCTCCCAGAAACTGAGACGxxxxxxxxxxxxxxxxxx |       10 |      35 |          45 |         34 |          1 |         1 |          1 |          0 |          0 | 38.5141 | 62.1654 |  62.1654 | -277.939 | 58.2253 | -340.105 |         7 |        16 |        23 |    70      |    45.7143 |    51.1111 |  -10.4 |   -0.6 |            45.9675 |         0.0826205 |
-|  4 | Sample | ATAAAAGACAACACCCTTGCCTTGTGGAGTTTTCAAAGCTCCCAGAAACTGAGAAGAACTATAACCTGCAAATG | xxxxxxxxxxACACCCTTGCCTTGTGGAGTTTTCAAAGCTCCCAGAAACTGAGACGxxxxxxxxxxxxxxxxxx |       11 |      35 |          46 |         34 |          1 |         1 |          1 |          0 |          0 | 40.8741 | 62.1654 |  62.1654 | -277.939 | 58.2253 | -340.105 |         7 |        16 |        23 |    63.6364 |    45.7143 |    50      |  -10.4 |   -0.6 |            45.9675 |         0.0910506 |
+|   | Target                                            | Spacer                         | RT-PBS                                         | PBSlen | RTlen | RT-PBSlen | Edit_pos | Edit_len | RHA_len | PE2max_score |
+| - | ------------------------------------------------- | ------------------------------ | ---------------------------------------------- | ------ | ----- | --------- | -------- | -------- | ------- | ------------ |
+| 0 | ATAAAAGACAACACCCTTGCCTTGTGGAGTTTTCAAAGCTCCCAGA... | ATAAAAGACAACACCCTTGCCTTGTGGAGT | CGTCTCAGTTTCTGGGAGCTTTGAAAACTCCACAAGGCAAGG     | 7      | 35    | 42        | 34       | 1        | 1       | 0.904907     |
+| 1 | ATAAAAGACAACACCCTTGCCTTGTGGAGTTTTCAAAGCTCCCAGA... | ATAAAAGACAACACCCTTGCCTTGTGGAGT | CGTCTCAGTTTCTGGGAGCTTTGAAAACTCCACAAGGCAAGGG    | 8      | 35    | 43        | 34       | 1        | 1       | 2.377118     |
+| 2 | ATAAAAGACAACACCCTTGCCTTGTGGAGTTTTCAAAGCTCCCAGA... | ATAAAAGACAACACCCTTGCCTTGTGGAGT | CGTCTCAGTTTCTGGGAGCTTTGAAAACTCCACAAGGCAAGGGT   | 9      | 35    | 44        | 34       | 1        | 1       | 2.613841     |
+| 3 | ATAAAAGACAACACCCTTGCCTTGTGGAGTTTTCAAAGCTCCCAGA... | ATAAAAGACAACACCCTTGCCTTGTGGAGT | CGTCTCAGTTTCTGGGAGCTTTGAAAACTCCACAAGGCAAGGGTG  | 10     | 35    | 45        | 34       | 1        | 1       | 3.643573     |
+| 4 | ATAAAAGACAACACCCTTGCCTTGTGGAGTTTTCAAAGCTCCCAGA... | ATAAAAGACAACACCCTTGCCTTGTGGAGT | CGTCTCAGTTTCTGGGAGCTTTGAAAACTCCACAAGGCAAGGGTGT | 11     | 35    | 46        | 34       | 1        | 1       | 3.770234     |
 
 
-
-It is also possible to predict other cell lines (A549, DLD1...) and PE systems (PE2max, PE4max...).
+#### if you wanna see biofeatures
 
 ```python
-from genet import predict as prd
+df_pe = prd.pe_score(seq_wt, seq_ed, alt_type, show_features=True)
+df_pe.head()
+```
+|   | ID     | WT74_On                                                                    | Edited74_On                                                                | PBSlen | RTlen | RT-PBSlen | Edit_pos | Edit_len | RHA_len | type_sub | type_ins | type_del | Tm1      | Tm2     | Tm2new  | Tm3       | Tm4      | TmD       | nGCcnt1 | nGCcnt2 | nGCcnt3 | fGCcont1 | fGCcont2 | fGCcont3 | MFE3   | MFE4  | DeepSpCas9_score | PE2max_score |
+| - | ------ | -------------------------------------------------------------------------- | -------------------------------------------------------------------------- | ------ | ----- | --------- | -------- | -------- | ------- | -------- | -------- | -------- | -------- | ------- | ------- | --------- | -------- | --------- | ------- | ------- | ------- | -------- | -------- | -------- | ------ | ----- | ---------------- | ------------ |
+| 0 | Sample | ATAAAAGACAACACCCTTGCCTTGTGGAGTTTTCAAAGCTCCCAGAAACTGAGAAGAACTATAACCTGCAAATG | xxxxxxxxxxxxxxCCTTGCCTTGTGGAGTTTTCAAAGCTCCCAGAAACTGAGACGxxxxxxxxxxxxxxxxxx | 7      | 35    | 42        | 34       | 1        | 1       | 1        | 0        | 0        | 16.19097 | 62.1654 | 62.1654 | \-277.939 | 58.22525 | \-340.105 | 5       | 16      | 21      | 71.42857 | 45.71429 | 50       | \-10.4 | \-0.6 | 45.96754         | 0.904907     |
+| 1 | Sample | ATAAAAGACAACACCCTTGCCTTGTGGAGTTTTCAAAGCTCCCAGAAACTGAGAAGAACTATAACCTGCAAATG | xxxxxxxxxxxxxCCCTTGCCTTGTGGAGTTTTCAAAGCTCCCAGAAACTGAGACGxxxxxxxxxxxxxxxxxx | 8      | 35    | 43        | 34       | 1        | 1       | 1        | 0        | 0        | 30.19954 | 62.1654 | 62.1654 | \-277.939 | 58.22525 | \-340.105 | 6       | 16      | 22      | 75       | 45.71429 | 51.16279 | \-10.4 | \-0.6 | 45.96754         | 2.377118     |
+| 2 | Sample | ATAAAAGACAACACCCTTGCCTTGTGGAGTTTTCAAAGCTCCCAGAAACTGAGAAGAACTATAACCTGCAAATG | xxxxxxxxxxxxACCCTTGCCTTGTGGAGTTTTCAAAGCTCCCAGAAACTGAGACGxxxxxxxxxxxxxxxxxx | 9      | 35    | 44        | 34       | 1        | 1       | 1        | 0        | 0        | 33.78395 | 62.1654 | 62.1654 | \-277.939 | 58.22525 | \-340.105 | 6       | 16      | 22      | 66.66667 | 45.71429 | 50       | \-10.4 | \-0.6 | 45.96754         | 2.613841     |
+| 3 | Sample | ATAAAAGACAACACCCTTGCCTTGTGGAGTTTTCAAAGCTCCCAGAAACTGAGAAGAACTATAACCTGCAAATG | xxxxxxxxxxxCACCCTTGCCTTGTGGAGTTTTCAAAGCTCCCAGAAACTGAGACGxxxxxxxxxxxxxxxxxx | 10     | 35    | 45        | 34       | 1        | 1       | 1        | 0        | 0        | 38.51415 | 62.1654 | 62.1654 | \-277.939 | 58.22525 | \-340.105 | 7       | 16      | 23      | 70       | 45.71429 | 51.11111 | \-10.4 | \-0.6 | 45.96754         | 3.643573     |
+| 4 | Sample | ATAAAAGACAACACCCTTGCCTTGTGGAGTTTTCAAAGCTCCCAGAAACTGAGAAGAACTATAACCTGCAAATG | xxxxxxxxxxACACCCTTGCCTTGTGGAGTTTTCAAAGCTCCCAGAAACTGAGACGxxxxxxxxxxxxxxxxxx | 11     | 35    | 46        | 34       | 1        | 1       | 1        | 0        | 0        | 40.87411 | 62.1654 | 62.1654 | \-277.939 | 58.22525 | \-340.105 | 7       | 16      | 23      | 63.63636 | 45.71429 | 50       | \-10.4 | \-0.6 | 45.96754         | 3.770234     |
+
 
-seq_wt   = 'ATGACAATAAAAGACAACACCCTTGCCTTGTGGAGTTTTCAAAGCTCCCAGAAACTGAGAAGAACTATAACCTGCAAATGTCAACTGAAACCTTAAAGTGAGTATTTAATTGAGCTGAAGT'
-seq_ed   = 'ATGACAATAAAAGACAACACCCTTGCCTTGTGGAGTTTTCAAAGCTCCCAGAAACTGAGACGAACTATAACCTGCAAATGTCAACTGAAACCTTAAAGTGAGTATTTAATTGAGCTGAAGT'
-alt_type = 'sub1'
+#### It is also possible to predict other cell lines (A549, DLD1...) and PE systems (PE2max, PE4max...).
 
+```python
 df_pe = prd.pe_score(seq_wt, seq_ed, alt_type, sID='MyGene', pe_system='PE4max', cell_type='A549')
 ```
 

diff --git a/genet/predict/functional.py b/genet/predict/functional.py
@@ -1022,8 +1022,8 @@ def get_extension(masked_seq:str):
         df['Target'] = df_all['WT74_On']
         df['Spacer'] = list_Guide30
         df['RT-PBS'] = df_all['Edited74_On'].apply(get_extension)
-        df['%s_score' % pe_system] = df_all['%s_score' % pe_system]
         df = pd.concat([df,df_all.iloc[:, 3:9]],axis=1)
+        df['%s_score' % pe_system] = df_all['%s_score' % pe_system]
 
         return df
 

diff --git a/genet/utils/__init__.py b/genet/utils/__init__.py
@@ -4,7 +4,7 @@
 # python setup.py bdist_wheel
 # twine upload dist/genet-0.5.2-py3-none-any.whl
 
-version_ = '0.8.0'
+version_ = '0.8.1'
 
 __version__ = version_