EMBL2checklists 0.6
Converts EMBL- or GenBank-formatted flatfiles to submission checklists (i.e., tab-separated spreadsheets) for submission to ENA via the interactive Webin submission system
License: BSD
Keywords: novel DNA sequences,public sequence databases,European Nucleotide Archive,file conversion,data upload

*EMBL2checklists*
=================

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EMBL2checklists converts EMBL- or GenBank-formatted flat files to submission-ready checklists (i.e., tab-separated spreadsheets) for submission to [ENA](http://www.ebi.ac.uk/ena) via the interactive [Webin submission system](https://www.ebi.ac.uk/ena/submit/sra/#home).


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## FEATURES
* Foo
* Bar
* Baz

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## INPUT, OUTPUT AND PREREQUISITES
* **Input**: EMBL- or GenBank-formatted flatfile
* **Output**: tab-separated spreadsheet ("checklist")
* **Prerequisites**: Input flatfiles must have the DNA marker name (e.g., "matK", "ITS") as qualifier value for any of the defined key_features ("gene", "note", "product" or "standard_name").


## EXAMPLE USAGE

### On Linux / MacOS

#### Commandline Interface
```
$ EMBL2checklists_CLI \
    -i example/input/example_trnK_matK.embl \
    -o example/temp/example_trnK_matK.tsv \
    -c trnK_matK \
    -e no
```
#### GUI Interface
```
$ EMBL2checklists_GUI
```

### On Windows

#### GUI Interface
Simply double-click the file `EMBL2checklist_GUI.exe` as generated during the installation (see below).


![](images/EMBL2checklist_GUI.png)


## INSTALLATION
First, please be sure to have [Python 2.7 installed](https://www.python.org/downloads/) on your system. Then:

To get the most recent stable version of *EMBL2checklists*, run:

    $ pip2 install EMBL2checklists

Or, alternatively, if you want to get the latest development version of *EMBL2checklists*, run:

    $ pip install git+https://github.com/michaelgruenstaeudl/EMBL2checklists.git


<!---

## CITATION
Using EMBL2checklists in your research? Please cite it!

- Gruenstaeudl M., Hartmaring Y. (2018). EMBL2checklists: A Python package to facilitate the user-friendly submission of plant and fungal DNA barcoding sequences to ENA. bioRxiv: 435644. https://www.biorxiv.org/content/early/2018/10/05/435644

```
@article {Gruenstaeudl435644,
    author = {Gruenstaeudl, Michael and Hartmaring, Yannick},
    title = {EMBL2checklists: A Python package to facilitate the user-friendly submission of plant DNA barcoding sequences to ENA},
    elocation-id = {435644},
    year = {2018},
    doi = {10.1101/435644},
    URL = {https://www.biorxiv.org/content/early/2018/10/05/435644},
    journal = {bioRxiv}
}
```

-->


## CHANGELOG
See [`CHANGELOG.md`](CHANGELOG.md) for a list of recent changes to the software.