semvec/pypi-packages huggingface dataset:
extract-specific-sites-from-msa 0.0.2
To extract some sites from a multiple sequence alignment. By Guanliang MENG, go to https://github.com/linzhi2013 for more details.
Requires Python: >=3

# extract_specific_sites_from_msa

## 1 Introduction

`extract_specific_sites_from_msa` is a tool to extract some sites (or codon) from a multiple sequence alignment.

## 2 Installation

    pip install extract_specific_sites_from_msa

There will be a command `extract_specific_sites_from_msa` created under the same directory as your `pip` command.

## 3 Usage

    usage: extract_specific_sites_from_msa [-h] [-infile <file>]
                                           [-format {fasta,emboss,stockholm,phylip,phylip-relaxed,clustal}]
                                           [-outformat {fasta,emboss,stockholm,phylip,phylip-relaxed,clustal}]
                                           [-outfile <file>] [-config <file>]
                                           [-codon <int>]

    To extract some sites (or codon) from a multiple sequence alignment. By
    Guanliang MENG, go to
    https://github.com/linzhi2013/extract_specific_sites_from_msa for more
    details.

    optional arguments:
      -h, --help            show this help message and exit
      -infile <file>        input multiple sequence alignment file
      -format {fasta,emboss,stockholm,phylip,phylip-relaxed,clustal}
                            input file format [phylip-relaxed]
      -outformat {fasta,emboss,stockholm,phylip,phylip-relaxed,clustal}
                            output file format [fasta]
      -outfile <file>       outfile
      -config <file>        a file containing the sites to be extracted (1 left-
                            based). do not support 2-5, you should write 2 3 4 5
                            instead, the site numbers in config can be on one line
                            or multiple lines.
      -codon <int>          codon site to be extracted [2]
        
## Author
Guanliang MENG

## Citation
Currently I have no plan to publish `extract_specific_sites_from_msa`.

However, since `extract_specific_sites_from_msa` makes use of Biopython, you should cite it if you use msaconverter in your work:

    Peter J. A. Cock, Tiago Antao, Jeffrey T. Chang, Brad A. Chapman, Cymon J. Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczynski, Michiel J. L. de Hoon: “Biopython: freely available Python tools for computational molecular biology and bioinformatics”. Bioinformatics 25 (11), 1422–1423 (2009). https://doi.org/10.1093/bioinformatics/btp163
Please go to http://www.biopython.org/ for more details.
RestIFindPy 0.0.5
基于Restplus实现同花顺iFinD接口分布式调用
Requires Python: >=3.5

# DIRestPlus
通过Flask-RESTPlus 构建接口框架，将Wind、iFinD、Choice等进行统一封装

### 外部环境依赖及安装配置

#### ifind 环境配置
```commandline
python "d:\IDE\iFinD\bin\x64\installiFinDPy.py" "D:\IDE\iFinD\bin"
```

#### 测试接口文件安装是否成功
```python
from iFinDPy import *
# 返回 D:\WSPych\RestIFindPy\venv\lib\site-packages\iFinDPy.pth
# 说明安装成功

# 登陆
thsLogin = THS_iFinDLogin("***","***")  # 0

thsDataDataPool  = THS_DataPool('block','2016-11-27;001005260','date:Y,security_name:Y,thscode:Y')
```
atgcN-count 0.0.1
To stat the counts and percentage of each base in fasta file
Requires Python: >=3

# atgcN_count

## 1 Introduction

`atgcN_count` is a tool to stat the counts and percentage of each base in fasta file.

## 2 Installation

    pip install atgcN_count

There will be a command `atgcN_count` created under the same directory as your `pip` command.

## 3 Usage

    usage: atgcN_count[-h] [-i <file>] [-v] [-d <int>] [-N]

    To stat the counts of each base in a fasta file.

    optional arguments:
      -h, --help  show this help message and exit
      -i <file>   input fasta file
      -v          also output statistics for each sequence [False]
      -d <int>    decimals for output result [2]
      -N          do not take non-ATGC bases into account when caculate percentage
                  [False]

## Author
Guanliang MENG

## Citation
Currently I have no plan to publish `atgcN_count`.