Parsers for (programmatic) read submission to European Nucleotide Archive (ENA).
Parses a .tsv file & converts to the equivalent .xml file.
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 |
| .. | .. | .. | .. | .. |
| .. | .. | .. | .. | .. |
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
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.