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2021-01-28Moving tools out of submodules (sorry!)Pjotr Prins
2021-01-26Add phylogeny workflowNjagi Mwaniki
Signed-off-by: Njagi Mwaniki <njagi@urbanslug.com>
2021-01-08GenBank: Fix normalization and depth differences with original recordsPjotr Prins
2021-01-08Set JSON indentationPjotr Prins
2021-01-08Get correct GenBank ID with version, see #122Pjotr Prins
2021-01-08FASTA file should not have leading spacePjotr Prins
2021-01-07Allow for xml and xml.gz filesPjotr Prins
2021-01-06cleaned utils.pyAndreaGuarracino
2021-01-06Pubseq fetch: sometimes a request times out. So repeat with intervals.Pjotr Prins
2021-01-05cleaning update-from-genbank.py; removed unused import from genbank-fetch-ids.pyAndreaGuarracino
2021-01-05cleaning genbank-fetch-ids.pyAndreaGuarracino
2021-01-05Fetching fixesPjotr Prins
2021-01-05Add option for fetching fastaPjotr Prins
2021-01-05fetch: do a straight dump of the original recordPjotr Prins
2021-01-05fetches original metadata from PubSeq/ArvadosPjotr Prins
2021-01-05API: fix returned record to include original metadataPjotr Prins
2021-01-05RenamePjotr Prins
2021-01-04mapping: no longer requires specimen file for genbank outputPjotr Prins
2021-01-04Removing refs. No point in guessing termsPjotr Prins
2021-01-04mapping sample_species using regexPjotr Prins
2021-01-04Started on normalizationPjotr Prins
2021-01-03genbank: specimen sourcePjotr Prins
2021-01-03genbank: more or less complete. Need to add collection methodPjotr Prins
2021-01-03genbank: deal with host, sex and agePjotr Prins
2021-01-03genbank: technology parsingPjotr Prins
2021-01-03genbank: submitter infoPjotr Prins
2021-01-03genbank: get authorsPjotr Prins
2021-01-03Move reference code to different file so it does not break pythonPjotr Prins
2021-01-02GenBank date parsingPjotr Prins
2021-01-02transform-genbank-xml2yamlfa.py refactoringPjotr Prins
2021-01-02transform-genbank-xml2yamlfa.py rewritePjotr Prins
2021-01-01genbank: minor fixesPjotr Prins
2021-01-01gzip outputPjotr Prins
2021-01-01update-from-genbank.pyPjotr Prins
2021-01-01genbank-fetch-ids.pyPjotr Prins
2021-01-01genbank-fetch-idsPjotr Prins
2021-01-01genbank: cleaning upPjotr Prins
2021-01-01genbank-fetch-ids simple callPjotr Prins
2021-01-01sparql: make use of pattern matchingPjotr Prins
2020-12-31Add commentPjotr Prins
2020-12-31Improve SPARQL query and commentsPjotr Prins
2020-12-31genbank: sparql-fetch-idsPjotr Prins
2020-12-31sparql: rename filePjotr Prins
2020-12-31genbank: started on SPARQL fetcherPjotr Prins
2020-12-31genbank: pseudo workflowPjotr Prins
2020-12-31genbank: headerPjotr Prins
2020-12-31genbank: split scriptPjotr Prins
2020-12-31genbank: moving script into workflow spacePjotr Prins
2020-11-21abPOA works better starting from shorter sequencespangenome_workflow_abpoaAndreaGuarracino
2020-11-21added abPOA workflow; typosAndreaGuarracino
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