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tsv2xmlParser

Parsers for (programmatic) read submission to European Nucleotide Archive (ENA).

Parses a .tsv file & converts to the equivalent .xml file.

createSampleXml.py

takes one tsv file as the argument; tsv has the format:

"alias" "date" "province" "isolateName" "GisaidID"
Run3zz_BC01 2020-11-19 somewhere north hCoV-19/Netherlands/xy-ZZZ-1001/2020 EPI_ISL_xyyxzz
Run3zz_BC02 2020-10-14 somewhere south hCoV-19/Netherlands/xy-ZZZ-1002/2020 EPI_ISL_xyyxzz
Run3zz_BC03 2020-11-18 somewhere south hCoV-19/Netherlands/xy-ZZZ-1003/2020 EPI_ISL_xyyxzz
Run3zz_BC04 2020-11-19 somewhere north hCoV-19/Netherlands/xy-ZZZ-1004/2020 EPI_ISL_xyyxzz
.. .. .. .. ..
.. .. .. .. ..

createRunXml.py and createExpXml.py

take one tsv file as the argument; tsv has the format:

"samAlias" "expAlias" "gzFile" "md5"
Run3zz_BCyy Exp_Run3zz_BCyy path_to_folder/Run3zz_BCyy.fastq.gz 5bc7e43c01f76709b2c0d89b1f50264b
Run3zz_BCyy Exp_Run3zz_BCyy path_to_folder/Run3zz_BCyy.fastq.gz acad7c8f729469556c58abd0f30c88cd
Run3zz_BCyy Exp_Run3zz_BCyy path_to_folder/Run3zz_BCyy.fastq.gz 6f7fed624f91cb4f8512b96c4d9b1dec
Run3zz_BCyy Exp_Run3zz_BCyy path_to_folder/Run3zz_BCyy.fastq.gz b0f2ca8884b6ff7e35563d055e9c7d1a
.. .. .. ..
.. .. .. ..

where path_to_folder/ is relative to the root directory in the user account of the ENA ftp drop-box.

Usage: python createRunXml.py runxy-yz.tsv produces the output runxy-yz.xml

(test) programmatic submission of samples, runs, and experiments

curl -u Webin-USER:PASS -F "SUBMISSION=@submission.xml" -F "RUN=@runxy-yz.xml" -F "EXPERIMENT=@expxy-yz.xml" "https://wwwdev.ebi.ac.uk/ena/submit/drop-box/submit/" >> runExpLog.txt 2>&1

runExpLog.txt file stores the progress and error logs

When tests are successful, replace the url https://wwwdev.ebi.ac.uk/ena/submit/drop-box/submit/ with https://www.ebi.ac.uk/ena/submit/drop-box/submit/ for publishing.