Metadata-Version: 2.1
Name: annonex2embl
Version: 0.7.5
Summary: Converts an annotated DNA multi-sequence alignment (in NEXUS format) to an EMBL flatfile for submission to ENA via the Webin-CLI submission tool
Home-page: https://github.com/michaelgruenstaeudl/annonex2embl
Author: Michael Gruenstaeudl, PhD
Author-email: m.gruenstaeudl@fu-berlin.de
License: BSD
Description: *annonex2embl*
        ==============
        
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        Converts an annotated DNA multi-sequence alignment (in [NEXUS](http://wiki.christophchamp.com/index.php?title=NEXUS_file_format) format) to an EMBL flatfile for submission to [ENA](http://www.ebi.ac.uk/ena) via the [Webin-CLI submission tool](https://ena-docs.readthedocs.io/en/latest/cli_05.html).
        
        
        ## INPUT, OUTPUT AND PREREQUISITES
        * **Input**: an annotated DNA multiple sequence alignment in NEXUS format; a comma-delimited metadata table
        * **Output**: a submission-ready, multi-record EMBL flatfile
        
        #### Requirements / Input preparation
        The annotations of a NEXUS file are specified via [SETS-block](http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Phylogenetics:_NEXUS_Format), which is located beneath a DATA-block and defines sets of characters in the DNA alignment. In such a SETS-block, every gene and every exon charset must be accompanied by one CDS charset. Other charsets can be defined unaccompanied.
        
        #### Example of a complete SETS-BLOCK
        ```
        BEGIN SETS;
        CHARSET matK_gene_forward = 929-2530;
        CHARSET matK_CDS_forward = 929-2530;
        CHARSET trnK_intron_forward = 1-928 2531-2813;
        END;
        ```
        
        #### Examples of corresponding DESCR variable
        ```
        DESCR="tRNA-Lys (trnK) intron, partial sequence; maturase K (matK) gene, complete sequence"
        ```
        
        ## EXAMPLE USAGE
        #### On Linux / MacOS
        ```
        SCRPT=$PWD/scripts/annonex2embl_launcher_CLI.py
        INPUT=examples/input/TestData1.nex
        METAD=examples/input/Metadata.csv
        OTPUT=examples/temp/TestData1.embl
        DESCR='description of alignment'  # Do not use double-quotes
        EMAIL=your_email_here@yourmailserver.com
        AUTHR='your name here'  # Do not use double-quotes
        MNFTS=PRJEB00000
        MNFTD=${DESCR//[^[:alnum:]]/_}
        
        python3 $SCRPT -n $INPUT -c $METAD -d "$DESCR" -e $EMAIL -a "$AUTHR" --productlookup True -o $OTPUT --manifeststudy $MNFTS --manifestdescr $MNFTD --compress True
        ```
        
        #### On Windows
        ```
        SET SCRPT=$PWD\scripts\annonex2embl_launcher_CLI.py
        SET INPUT=examples\input\TestData1.nex
        SET METAD=examples\input\Metadata.csv
        SET OTPUT=examples\temp\TestData1.embl
        SET DESCR='description of alignment'
        SET EMAIL=your_email_here@yourmailserver.com
        SET AUTHR='your name here'
        SET MNFTS=PRJEB00000
        SET MNFTD=a_unique_description_here
        
        python %SCRPT% -n %INPUT% -c %METAD% -d %DESCR% -e %EMAIL% -a %AUTHR% --productlookup True -o %OTPUT% --manifeststudy %MNFTS% --manifestdescr %MNFTD% --compress True
        ```
        
        ## INSTALLATION
        First, please be sure to have [Python 3 installed](https://www.python.org/downloads/) on your system. Then:
        
        To get the most recent stable version of *annonex2embl*, run:
        
            pip install annonex2embl
        
        Or, alternatively, if you want to get the latest development version of *annonex2embl*, run:
        
            pip install git+https://github.com/michaelgruenstaeudl/annonex2embl.git
        
        ## TESTING
        #### Regular testing
        
            python3 setup.py test
            pytest  # alternative
        
        #### Testing for development
        To run the unittests outside of 'python setup.py test':
        
            python3 -m unittest discover -s tests -p "*_test.py"
        
        <!--
        ## TO DO
        * Implement improved argparse code: Currently, --taxcheck requires "True" of "False" as parameters. Please modify so that only the presence of --taxcheck indicates "True", whereas its abscence indicates "False".
        * Implement improved argparse code: Currently, the software incorrectly says "optional parameters" for all parameters upon execution via `python scripts/annonex2embl_launcher_CLI.py -h`. Please modify so that it correctly differentiates between "required" and "optional" parameters.
        -->
        
        ## 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,flatfile
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3.7
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
