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Export of results #28

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rneher opened this issue Jun 26, 2020 · 2 comments
Closed

Export of results #28

rneher opened this issue Jun 26, 2020 · 2 comments
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good first issue Good for newcomers help wanted Extra attention is needed prio:high Do this immediately t:feat Type: request of a new feature, functionality, enchancement

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@rneher
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rneher commented Jun 26, 2020

The current export returns a json structure which contains the results, along with a bunch of other things (like processing status, redundant clade definitions, etc). Most users will want to export a file they can view, share, and analyze in Excel or similar.

I think a tsv table with the following columns would address most needs:

sequenceName
clade
alignmentStart
alignmentEnd
numberOfMutations
numberOfNonACGTN
numberOfN
mutations: C242T,C14408T,A24304G,..
deletions: 567-572,23304-20423,...
insertions: 678:ACG,23565:GTGTCG,...
missing: 16121-16525,27343-27565,...
QC-Fail/Pass
QC-flags: 'too many mutations','SNP clusters'

Some of the fields are themselves arrays (like the mutations) and hence a table is not ideal. But if we provide json export as well, I think we address most needs.
@ivan-aksamentov
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ivan-aksamentov commented Jun 27, 2020 •
edited

TODO:

  • remove redundant items from JSON export
  • implement TSV export as specified above

@ivan-aksamentov ivan-aksamentov added t:feat Type: request of a new feature, functionality, enchancement good first issue Good for newcomers help wanted Extra attention is needed labels Jun 28, 2020
@rneher rneher added the prio:high Do this immediately label Jun 28, 2020
@ivan-aksamentov ivan-aksamentov mentioned this issue Jun 30, 2020
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@ivan-aksamentov
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Resolved in #51

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good first issue Good for newcomers help wanted Extra attention is needed prio:high Do this immediately t:feat Type: request of a new feature, functionality, enchancement
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