https://github.com/tjarkdoering/tdnamagic

Shell script to complement TDNAscan in some minor way.
https://github.com/tjarkdoering/tdnamagic

Last synced: 1 day ago
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Shell script to complement TDNAscan in some minor way.

• Host: GitHub
• URL: https://github.com/tjarkdoering/tdnamagic
• Owner: tjarkdoering
• License: gpl-3.0
• Created: 2021-04-27T13:34:29.000Z (almost 4 years ago)
• Default Branch: main
• Last Pushed: 2021-04-30T09:24:54.000Z (almost 4 years ago)
• Last Synced: 2024-11-29T17:45:26.084Z (2 months ago)
• Language: Shell
• Size: 22.5 KB
• Stars: 0
• Watchers: 0
• Forks: 0
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# TDNAmagic

Shell script to complement TDNAscan in some minor way. To be more precise, it allows you to call [TDNAscan](https://github.com/noble-research-institute/TDNAscan) from the working directory you are in and receive the results into the very same one. Without the fuss of cleaning up your TDNAscan directory.

## Usage

1. Make sure your TDNAscan is working. Invoke `python tdnascan.py --version` from the TDNAscan directory or something.

2. Move the script to any of your `bin` path (so you can invoke it from anywhere) and make it executable. Preferably of any of the user accessible ones. Or just add an alias to whatever-shell-you-have initialization file or add a symlink to it into your user `bin` path. So many options. Be creative.

3. Open the script in an editor of your choice and add the path to your TDNAscan dir and check the contents that it doesn't do anything malicious.

4. Change `nameofthatfile` to the file that is always in the wrong spot.

4. Navigate to your working directory (containing your the two paired read files, the T-DNA sequence file and the genome sequence file).

5. Call the script:

```

$ tdnamagic.sh -1 forward.fq -2 reverse.fq -t t-dna.fa -g ref_genome.fa

```

## Troubles using this?

Feel free to contact me or any of your resident bioinformaticians :wink: