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
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.
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