Comments (6)
@FedeGueli Hi Federico,
This sounds useful.
Just to understand your use-case better, do you need to see some sort of an aggregate statistics, such as:
- clade "A": 3 sequences
- clade "B": 10 sequences
- clade "C": 4 sequences
- total: 17 sequences
?
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Thanks Ivan! that sounds great! but if it is too time expending it is enough a fixed column with 1 2 3 4 where i can count number of sequences belonging to a sublineage after sorting for example for unaliased lineage:
1-10 BA.5.1 = 10
11-16 Ba.5.2 = 6 and so on.
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@FedeGueli I implemented a prototype in #1092
A preview app can be tested here: https://nextclade-git-feat-web-row-index-nextstrain.vercel.app/
Is this what you wanted?
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@FedeGueli I implemented a prototype in #1092
A preview app can be tested here: https://nextclade-git-feat-web-row-index-nextstrain.vercel.app/
Is this what you wanted?
Perfect!! It is exactly what i was meaning!
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@FedeGueli In #1096 I made a prototype of simple clade statistics. Is this something that can help your use-case?
Here is a preview app: https://nextclade-git-feat-web-clade-stats-nextstrain.vercel.app/
The layout is not perfect yet and there might be bugs.
The team is hesitant to add complex post-processing features like this, so I don't guarantee it appears in the main app. But if there's strong need, it will be easier to justify.
P.S. By "post-processing" I mean that the same results can be easily generated by downloading the TSV output file, opening it in Excel and plotting the charts you need or processing it in any way you like in Excel or with Python & pandas etc.
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Hi Ivan! Sincerely i found your #1096 very good to visualize immediately results, and for the purpose to scan for variants it can help a lot while scanning big batches of sequences. if it is handy why not i would say? but obviously i understand that it is a duplicate of things easy to do with the TSV. Sincerely i dont think i am the right person to talk about this kind of things i ignored the existance and use of the buttons there, really cool to know them now.
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Related Issues (20)
- Incorporation of enterovirus dataset into nextalde docker container HOT 1
- Include aligned sequences and translations in ndjson
- ENH(nextalign cli): show default values in --help usage statement HOT 4
- Maximum Sequence Limit? HOT 2
- Web: Grey scale coloring for region/country/divison if scale not predefined in reference tree HOT 5
- How to decide if the reversionSubstitutions are valid variants or not and whether to keep them? HOT 2
- Direct Auspice SVG Download
- ENH: enlarge Visualization when more nucleotides/Codons even if mutations not fall in striclty adjacent codons but close enough to need a whole view. HOT 2
- Updating certain parts of the JSON file output from Map to Array HOT 2
- linux-musl artefact gets slower rather than faster when parallelizing in contrast to gnu HOT 5
- Parsing PCR primers HOT 2
- how many SARS-COV-2 sequences can nextclade handle in a MSA file? HOT 8
- Is there any example for handling HIV data? HOT 2
- Web crash: The target <seqName> could not be identified in the dom HOT 2
- Show "browser not supported HOT 1
- Show "browser not supported" modal only once per session HOT 3
- if the qc.overallStatus of my sequences are mediocre, can we keep them for next step analysis? HOT 5
- web-based nextclade issue when using another reference HOT 8
- web(minor): when customizing dataset files, it always says "pasted sequences" even if the field is for tree HOT 2
- I upload 1490 sequences to nextclade, and upload to auspice.us, why it shows me 4255 sequences? HOT 2
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