Converts an annotated DNA multi-sequence alignment (in NEXUS format) to an EMBL flatfile for submission to ENA via the Webin-CLI submission tool
Project description
annonex2embl
Converts an annotated DNA multi-sequence alignment (in NEXUS format) to an EMBL flatfile for submission to ENA via the Webin-CLI submission tool.
INSTALLATION
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
INPUT, OUTPUT AND PREREQUISITES
- Input: an annotated DNA multiple sequence alignment in NEXUS format; and a comma-delimited (CSV) metadata table
- Output: a submission-ready, multi-record EMBL flatfile
Requirements / Input preparation
The annotations of a NEXUS file are specified via SETS-block, 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=$PWD/scripts/annonex2embl_launcher_CLI.py
INPUT=examples/input/TestData1.nex
METAD=examples/input/Metadata.csv
OTPUT=examples/temp/TestData1.embl
DESCR='description of alignment here' # Do not use double-quotes
EMAIL=your_email_here@yourmailserver.com
AUTHR='your name here' # Do not use double-quotes
MNFTS=PRJEB00000
MNFTD=${DESCR//[^[:alnum:]]/_}
python3 $SCRPT -n $INPUT -c $METAD -d "$DESCR" -e $EMAIL -a "$AUTHR" -o $OTPUT --productlookup --manifeststudy $MNFTS --manifestdescr $MNFTD --compress
On Windows
SET SCRPT=$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 here'
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% -o %OTPUT% --productlookup --manifeststudy %MNFTS% --manifestdescr %MNFTD% --compress
TO DO
Would it be possible to have the CDS definition of Taxon 4 in TestData2.embl changed from "complement(join(19..27,<11..16))" to "complement(join(<11..16,19..27))", while the automatic translation remains "MLSLL"? (I know that we chatted about it, but I don't remember the precise discussion anymore. Something about the meaning of "complement".) If it is possible, then please adjust the code accordingly. If not, then please write down an explanation sentence for me as to why that would mess up the translation.Currently the output is "complement(join(<11..16,19..27))"
CHANGELOG
See CHANGELOG.md
for a list of recent changes to the software.
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