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Converts EMBL- or GenBank-formatted flatfiles to submission checklists (i.e., tab-separated spreadsheets) for submission to ENA via the interactive Webin submission system

Project description

EMBL2checklists

PyPI status PyPI pyversions PyPI version shields.io PyPI license

EMBL2checklists converts EMBL- or GenBank-formatted flatfiles to submission checklists (i.e., tab-separated spreadsheets) for submission to ENA via the interactive Webin submission system.

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/example_trnKmatK.embl \
    -o example/example_trnKmatK.tsv \
    -c trnK_matK \
    -e no

GUI Interface

$ EMBL2checklists_GUI

On Windows

GUI Interface

Simply double-click the file EMBL2checklist_GUI.exe

INSTALLATION

First, please be sure to have Python 2.7 install installed 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

CHANGELOG

See CHANGELOG.md for a list of recent changes to the software.

Project details


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