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More + more accurately named clonal family fasta downloads #143

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eharkins opened this issue Jul 19, 2019 · 0 comments
Open

More + more accurately named clonal family fasta downloads #143

eharkins opened this issue Jul 19, 2019 · 0 comments
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@eharkins
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As it is now we have:

  • "Download Fasta: Unique Sequences In This Tree" which is named like <clonal_family.id>.fasta
  • " Download Fasta: Lineage Sequences" which is named like <lineage_sequence.id>-lineage.fasta

In a recent meeting with @lauradoepker, we settled on the following options instead (names of buttons tbd but behavior and file names are what's important):

  • Download tree sequences: Should include ASR + leaves and file should be labeled with -indels-reversed if the sequences from partis used came from the inde_reversed_seqs key
  • Download original leaves: Should include only non-indel-reversed original sampled sequences from the cluster from the partis input_seqs key. (Should we label to emphasize non-indel-reversed status?)
  • Download lineage: Should include lineage sequences from selected sequence to naive, and file name should reflect indel status in the same way as the tree sequences by adding -indels-reversed if the indel_reversed_seqs key was used from the partis output for any of the cluster sequences
@eharkins eharkins self-assigned this Jul 19, 2019
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