Metadata-Version: 2.1
Name: EMBL2checklists
Version: 0.6
Summary: Converts EMBL- or GenBank-formatted flatfiles to submission checklists (i.e., tab-separated spreadsheets) for submission to ENA via the interactive Webin submission system
Home-page: https://github.com/michaelgruenstaeudl/EMBL2checklists
Author: Michael Gruenstaeudl, PhD
Author-email: m.gruenstaeudl@fu-berlin.de
License: BSD
Description: *EMBL2checklists*
        =================
        
        [![Build Status](https://ci.appveyor.com/api/projects/status/github/michaelgruenstaeudl/EMBL2checklists?branch=master&svg=true)](https://ci.appveyor.com/api/projects/status/github/michaelgruenstaeudl/EMBL2checklists)
        [![Build Status](https://travis-ci.com/michaelgruenstaeudl/EMBL2checklists.svg?branch=master)](https://travis-ci.com/michaelgruenstaeudl/EMBL2checklists)
        [![PyPI status](https://img.shields.io/pypi/status/EMBL2checklists.svg)](https://pypi.python.org/pypi/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).
        
        
        <!---
        
        ## FEATURES
        * Foo
        * Bar
        * Baz
        
        -->
        
        
        ## 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.
        
Keywords: novel DNA sequences,public sequence databases,European Nucleotide Archive,file conversion,data upload
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python :: 2.7
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
