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https://github.com/adamtaranto/ltr-harvest-reformat
Correct sequence names in LTR_Harvest GFF3 output.
https://github.com/adamtaranto/ltr-harvest-reformat
Last synced: 3 days ago
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Correct sequence names in LTR_Harvest GFF3 output.
- Host: GitHub
- URL: https://github.com/adamtaranto/ltr-harvest-reformat
- Owner: Adamtaranto
- License: mit
- Created: 2017-05-04T10:09:17.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2017-09-19T05:06:49.000Z (over 7 years ago)
- Last Synced: 2024-11-21T02:33:38.925Z (2 months ago)
- Language: Python
- Size: 2.93 KB
- Stars: 2
- Watchers: 3
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# LTR-Harvest-Reformat
Correct sequence names in LTR_Harvest GFF3 output.
# Contents
* [Options and usage](#options-and-usage)
* [Installing LTR-HR](#installing-ltr-hr)
* [Example usage](#example-usage)
* [Standard options](#standard-options)
* [License](#license)
# Options and usage
## Installing LTR-HR
Clone from this repository:
```bash
git clone https://github.com/Adamtaranto/LTR-Harvest-Reformat.git && cd LTR-Harvest-Reformat
```
## Example usage
```bash
./LTR-Harvest-Reformat.py -i LTR_Harvest_annot.gff3 -d results -o renammed_LTR_Harvest_annot.gff3
```
**Output:**
- results/renammed_LTR_Harvest_annot.gff3
## Standard options
```
Usage: ./LTR-Harvest-Reformat.py [-h] [--version] -i INFILE [-d OUTDIR] [-o GFFOUT]
Correct sequence names in LTR_Harvest GFF3 output.
optional arguments:
-h, --help Show this help message and exit.
--version Show program's version number and exit.
-i, --infile GFF3 file from LTR_Harvest.
-d, --outDir Optional: Set output directory.
-o, --gffOut Optional: Set alternative name for output file.
```
# License
Software provided under MIT license.