https://github.com/josttim/transnetyx-pyrat-utils

https://github.com/josttim/transnetyx-pyrat-utils

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• Host: GitHub
• URL: https://github.com/josttim/transnetyx-pyrat-utils
• Owner: JostTim
• Created: 2024-11-05T15:08:42.000Z (2 months ago)
• Default Branch: main
• Last Pushed: 2024-11-05T15:25:25.000Z (2 months ago)
• Last Synced: 2024-11-05T16:36:27.372Z (2 months ago)
• Language: Python
• Size: 7.81 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# transnetyx-pyrat-utils

Export your transnetyx genotyping results as a .csv file.

## Python

Just supply the name of the file you have in your Downloads folder, and run ``.convert()``

```python

from transnetyx_pyrat_utils import Converter

converter = Converter("OrderResults-2215183-638663954144327998.csv").convert()

```

## CLI 

```bash

pdm run transpyrat OrderResults-2215183-638663954144327998.csv

```

or 

```bash

pdm run transpyrat -f OrderResults-2215183-638663954144327998.csv

```

or 

```bash

pdm run transpyrat --file OrderResults-2215183-638663954144327998.csv

```

get the full help with

```bash

pdm run transpyrat --help

```

⤵️

```bash

Usage: -c [-h] [-f FILE] [file]

Positional Arguments:

  file                  The file name or path leading to the file to be converted. By default, the file name is searched for    

                        in the Downloads folder of the current user's home.

Options:

  -h, --help            show this help message and exit

  -f, --file FILE       The file name or path leading to the file to be converted. By default, the file name is searched for    

                        in the Downloads folder of the current user's home.

```

## Config

As you have more lines and strains to convert from transnetyx framework intopyrat one, add these strains in the `transnetyx_config.json` configuration file, that sits in the source code folder of this package. (it can also be supplied from a different path, externally, by changing the transnetyx_config_filename or pyrat_config_filename attributes of your converter object, after instanciating it with a filename, and before running ``.convert()``)