Qi Fang

Parameter optimization for non-model species (max gene size and so on)

6

Hi Gotoh, Recently, I'm trying to replace genewise with your spaln. I found spaln could get more expected gene structure as query protein. It seems great! To apply in non-model...

two errors of gff3 output

1

First, some results would be converted to 0-based start in gff3 output. I think it's the fault with the deletion of the first base. For example:  the gff3 output:...

PrinCurve_method needs specific tensorflow

1

`st.tdr.models.models_backbone.backbone_methods.PrinCurve_method` run into errors with newest `tensorflow`. It's necessary to use `tensorflow==2.11.0 keras==2.11`. Error reports: ``` File ~/miniconda3/envs/spateo_updated/lib/python3.9/site-packages/spateo/tdr/models/models_backbone/backbone_methods.py:116, in NLPCA.create_model(self, num_dim, nodes, lr) 113 # Create layers: 114 # Function...

missing dict in morphofield_gp

1

when run `morphofield_gp`, I found there is no `norm_dict` and `kernel_dict ` in [`morpho_class.py`](https://github.com/aristoteleo/spateo-release/blob/22220c57f8d501663be23c8f948dd310b505ca3d/spateo/alignment/methods/morpho_class.py#L1472C18-L1472C24) ``` File ~/miniconda3/envs/spateo/lib/python3.9/site-packages/spateo/tdr/morphometrics/morphofield/gaussian_process.py:102, in _gp_velocity(X, vf_dict) 100 def _gp_velocity(X: np.ndarray, vf_dict: dict) -> np.ndarray: 101 #...