semvec/pypi-packages huggingface dataset:
evydcloud 1.0.0
EvydenceCloud
Requires Python: >=3.7

# Tools for Evydence Cloud


## Getting Started

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See deployment for notes on how to deploy the project on a live system.

### Prerequisites

What things you need to install the software and how to install them

```
Give examples
```

### Installing

A step by step series of examples that tell you have to get a development env running

Say what the step will be

```
Give the example
```

And repeat

```
until finished
```

End with an example of getting some data out of the system or using it for a little demo

## Running the tests

Explain how to run the automated tests for this system

### Break down into end to end tests

Explain what these tests test and why

```
Give an example
```

### And coding style tests

Explain what these tests test and why

```
Give an example
```

## Deployment

Add additional notes about how to deploy this on a live system

## Built With

* [Dropwizard](http://www.dropwizard.io/1.0.2/docs/) - The web framework used
* [Maven](https://maven.apache.org/) - Dependency Management
* [ROME](https://rometools.github.io/rome/) - Used to generate RSS Feeds

## Contributing

Please read [CONTRIBUTING.md](https://gist.github.com/PurpleBooth/b24679402957c63ec426) for details on our code of conduct, and the process for submitting pull requests to us.

## Versioning

We use [SemVer](http://semver.org/) for versioning. For the versions available, see the [tags on this repository](https://github.com/your/project/tags).

## Authors

* **Billie Thompson** - *Initial work* - [PurpleBooth](https://github.com/PurpleBooth)

See also the list of [contributors](https://github.com/your/project/contributors) who participated in this project.

## License

This project is licensed under the MIT License - see the [LICENSE.md](LICENSE.md) file for details

## Acknowledgments

* Hat tip to anyone who's code was used
* Inspiration
* etc
RWexptest 0.0.14
A small example package
Requires Python: >=3.7

# RWexptest

This is a simple example package.

## Pseqpa

这个工具包是用于对蛋白质序列进行简单处理的工作，其中涉及的主要函数功能有：

### excel_csv_to_fasta

```python
from RWexptest import Pseqpa

# 指定输入和输出文件夹路径
input_folder = "<需要转换的目标文件的路径>"
output_folder = "<保存路径>"
entry_column_name = "Entry"  # 请替换为您的entry列的名称
sequence_column_name = "Sequence"  # 请替换为您的sequence列的名称

# 调用函数并传递输入和输出文件夹路径
excel_csv_to_fasta(input_folder, output_folder, entry_column_name, sequence_column_name)
```

### process_fasta_files

```python
from RWexptest import Pseqpa

# 指定输入目录、输出目录、批次大小以及最小和最大蛋白质序列长度
input_directory = "<fasta格式文件路径>"
output_directory = "<处理后的保存路径>"
batch_size = 500 #将fasta格式蛋白质序列按500个进行一次划分
min_sequence_length = 10 #筛选蛋白质序列最低不能小于10个氨基酸
max_sequence_length = 6000 #筛选蛋白质序列最高不能超过6000个氨基酸

# 处理fasta文件并将其分成批次，只保留符合长度条件的序列
process_fasta_files(input_directory, output_directory, batch_size, min_sequence_length, max_sequence_length)
```

### create_blast_database（需要你的终端环境已经配置好了NCBI Blast工具）

```python
from RWexptest import Pseqpa

# 指定构建数据库对象、数据库位置和数据库类型
input_fasta_path = "<your_train_data_path/train_data.fasta>" #路径不能有空格，路径必须是英文
output_db_path = "<Blast_database_path/Train_protein_seq_database>" #路径不能有空格，路径必须是英文
dbtype = "prot"  # 蛋白质数据库

# 构建数据库
result_message = create_blast_database(input_fasta_path, output_db_path, dbtype)
```

### run_blastp（需要你的终端环境已经配置好了NCBI Blast工具）

```python
from RWexptest import Pseqpa

# 指定balst对象、数据库、结果目录和结果格式
query_fasta_path = "<your_test_data_path/test_data.fasta>" #路径不能有空格，路径必须是英文
blast_db_path = "<Blast_database_path/Train_protein_seq_database>" #路径不能有空格，路径必须是英文
output_file_path = "<your_save_path/test_data_blast_results.xml>" #路径不能有空格，路径必须是英文
custom_outfmt = 5  # 自定义输出格式

#进行同源性blast
result_message = run_blastp(query_fasta_path, blast_db_path, output_file_path, custom_outfmt)
```

### execute_blast_workflow（需要你的终端环境已经配置好了NCBI Blast工具）

```python
from RWexptest import Pseqpa

# 指定相关路径
input_fasta_path = "<your_train_data_path/train_data.fasta>" #路径不能有空格，路径必须是英文
output_db_path = "<Blast_database_path/Train_protein_seq_database>" #路径不能有空格，路径必须是英文
query_fasta_path = "<your_test_data_path/test_data.fasta>" #路径不能有空格，路径必须是英文
custom_outfmt = 5 #路径不能有空格，路径必须是英文
dbtype = "prot" #或者
xml_result_path = "<your_save_path/test_data_blast_results.xml>"  # 自定义XML结果的保存位置，路径不能有空格，路径必须是英文

# 一次性完成数据库的创建和blast工作并获得xml文件
result = execute_blast_workflow(input_fasta_path, output_db_path, dbtype, query_fasta_path, custom_outfmt, xml_result_path)
```

### parse_blast_xml_to_excel

```python
import pandas as pd
from Bio import SearchIO
from RWexptest import Pseqpa

# 调用函数并传递输入XML文件和输出Excel文件的路径
input_xml = '<经过NCBI Blast处理后获得的xml文件路径/result.xml>' #路径不能有空格，路劲必须是英文
output_excel = '<保存路径/reuslt.xlsx>' #路径不能有空格，路劲必须是英文

parse_blast_xml_to_excel(input_xml, output_excel)
```