EMBL2checklists

EMBL2checklists

EMBL2checklists converts EMBL- or GenBank-formatted flat files to submission-ready 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/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).

INSTALLATION

First, please be sure to have Python 2.7 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.