semvec/pypi-packages huggingface dataset:
plastidUtilis 0.0.5
chloroplast/mitochondrion annotation toolkits
Requires Python: >=3.8

# plastidUtilis

`plastidUtilis` is a collection utilities of module which could be applied in manual annotation of plastid genome.



## How to get it?

```shell
# pip install biopython
pip install plastidUtilis
```



## How to use it?

Note: this toolkit is only compatible with TBtools, so be careful with other format in this version.

```shell
# main utilities
python -m plastidUtilis.Sort -f <Geseq_out_seq> -o <name_of_output> --header <Input_header>
python -m plastidUtilis.AbnormalDetect -a <input_fasta> -o <output_filename>
python -m plastidUtilis.BLAST -d <tRNA_database> -t <sort_tRNA> -o <output.fasta>
python -m plastidUtilis.Table2GBK -t <self-made table file> -o <.gb>
python -m plastidUtilis.Filter -f <input_fasta> -i <minumum_length> -I <maximum_length> -o <output filename>
python -m plastidUtilis.Longest -f <input.fasta> -d <delimiter> -o <output.fasta>

# side utilities
python -m plastidUtilis.Translate -i <sorted_CDS> -o <output_protein_sequence>
python -m plastidUtilis.Stats -i <sorted_CDS>    # further it will be designed as tabular output 
python -m plastidUtilis.SequenceAppend -f <input_assembly> -i <input_abnormal_bed> -n <the_number_of_extending_bp> -o <output>
```



# Pipeline





# License

MIT License
Copyright (c) 2022 Zihao Huang, Youpu-Chen.
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
pyerp 0.0.4
python library for Event-Related Potentials (ERPs) analysis
Requires Python: >=3.6

# scab-python
python library for Event-Related Potentials (ERPs) analysis


# Instruction
```python
eeg_files = list()
eeg_files.append(["NAME_OF_FILE_WITHOUT_EXTENTION", "TASK_NAME"])
```

```python
marker = list()
marker.append([101, "nontarget", "word1"])
marker.append([102, "nontarget", "word2"])
marker.append([103, "nontarget", "word3"])
marker.append([104, "nontarget", "word4"])
marker.append([105, "nontarget", "word5"])
marker.append([106, "nontarget", "word6"])
marker.append([111, "target", "word1"])
marker.append([112, "target", "word2"])
marker.append([113, "target", "word3"])
marker.append([114, "target", "word4"])
marker.append([115, "target", "word5"])
marker.append([116, "target", "word6"])
marker.append([210, "new-trial"])
```

# Requirments
mne version should be greater than 1.2
solve-errors 1.0.11
An automated package that solves basic python errors
Requires Python: >=3.6

# Error Solver

![PyPI - Python Version](https://img.shields.io/pypi/pyversions/error_solver.svg)
![PyPI](https://img.shields.io/pypi/v/error_solver.svg)
[![Build Status](https://travis-ci.com/mpewsey/error_solver.svg?branch=master)](https://travis-ci.com/mpewsey/error_solver)
[![Documentation Status](https://readthedocs.org/projects/error-solver/badge/?version=latest)](https://error-solver.readthedocs.io/en/latest/?badge=latest)
[![codecov](https://codecov.io/gh/mpewsey/error_solver/branch/master/graph/badge.svg)](https://codecov.io/gh/mpewsey/error_solver)

## About

This package contains classes and methods to automatically identify errors with python packages and solve it. The package catchs any errors related to the execeution of the script and try to automatically solve it. If it does not succes the package add lots of verbosity to identify where the error comes from and how to solve it. Very useful tool for debugging python scripts. 

## Installation

This package may be installed via pip:

```
pip install solve-errors
```

The above installation only install the dependencies required for the
`ErrorSolverPy` class. To also install the dependencies necessary for the
`ErrorSolver` class, use the following command instead:

```
pip install error_solver[all] solve-errors
```
## Installation bug

If the package is working well, contact us to leave a comment or try installing the package using Administrator level rights.

## Example: Error in Cylinder

The below example determines the propagation error tolerances for the cross sectional
area `A` and volume `V` of a cylinder given the measurement tolerance for the radius
`r` and height `h`.

```python
from error_solver import ErrorSolver
import solve-errors

# Define the equations
EQUATIONS = [
    'A = pi * r**2',
    'V = A * h'
]

# Solve the equations by some means and assemble the values in a dictionary
values = {
    'h': 12,
    'r': 5,
    'A': 78.54,
    'V': 942.48
}

# Define the known error tolerances
errors = {
    'h': 0.05,
    'r': 0.05
}

solver = solve-errors.ErrorSolver(EQUATIONS)
solver.solve(values, errors)
#           value      error  pct_error  is_calc
# var
# A     78.539816   1.570796   2.000000     True
# V    942.477796  22.776547   2.416667     True
# h     12.000000   0.050000   0.416667    False
# r      5.000000   0.050000   1.000000    False
```