Comments (9)
Updated in bioconda now: bioconda/bioconda-recipes#37140
from hamronization.
Great! Thanks for your patience!
It should already be automatically updating on pypi, dockerhub, and (pending the attentiveness of bioconda bot) updated on bioconda at some point today.
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(although it does seem the badges on the README aren't updating for some reason...)
from hamronization.
Ah damn, sorry, I thought I'd solved that issue/covered it with tests. I thought the concatenation should be adding those fields but I'll try initialising the empty combined dataframe earlier.
Does the same error occur if you run hamronize summarize
on just WAL001-megahit.mapping.potential.ARG.deeparg.json
or only with the big list of jsons?
If the former could you send me just that output file (to [email protected]) and if the latter the big ole zip?
from hamronization.
Yes, only WAL001-megahit, but strangely it seems to happen in all cases, e.g. VLC009-metaspades.mapping.potential.ARG.deeparg.json
which does have hits.
I'll send you the zip and you can test everything. Happy to also test any dev versions!
from hamronization.
This seems to work now but please test in your workflow. Instead of trying to add additional columns if needed post-concatenation, I now just initialise an empty dataframe with all the headers in summarize before concatenating.
One question to make sure I haven't failed to fix another issue: These input jsons to summarize weren't cached and not regenerated with the hamronization v1.1.0 right? hamronization should now be generating valid empty jsons (i.e., just files containing []
) when parsing empty tool reports but I see these files still have the ]
malformation.
from hamronization.
- OK! I will test this :)
- Ah yes correct sorry, the JSONs in the ZIP were still from 1.0.3 - It took a few days for the pipeline to run, so didn't want to run the whole thing again with 1.1.0 to find the same/different summarize issue 😅 . I can try to take a few and re-generate them with 1.1.0 to double check now though
from hamronization.
@fmaguire I can confirm 761fe77 fixes the bug, and that re-running e.g. harmonizate deeparg
on an 'empty' outputfile produces the correct empty JSON of []
.
Once this version is released on bioconda (I sped that up for 1.1.0 this morning btw 😬 ), I will update our nf-core nextflow module and re-run the full pipeline again and let you know how well it performs.
This issue can be closed now!
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oh and thanks for the quick turnaround :D
from hamronization.
Related Issues (20)
- help understanding resfinder run HOT 1
- ORF_ID missing once RGI report hAMRonized HOT 1
- RgiIO.py: Typo in line 79 HOT 1
- Fix issue of very similar runs falsely combining results in summary
- Genetic_variation_type HOT 1
- hamronize summarize - local variable 'parsed_report' reference before assignment HOT 3
- Flag overlapping ranges in hAMRonization
- AMR Variant detection - Parsers to be updated HOT 1
- Obtain specification field data information from JSON schema HOT 1
- Update README
- Add xlsx output HOT 1
- Add CONTRIBUTING.md
- Add fARGene
- PyPi not updated, 1.0.4 tarball reports version 1.0.3 HOT 2
- [BUG] Generated output does not follow CSP rules HOT 1
- Request for Zenodo archive
- [BUG] - RGI bwt gene_mapping HOT 3
- Updating version support for starmar, amrfinderplus, kmerresistance - summarize output breaks HOT 4
- nucleotide specific fileds are empty while importing AmrFinderPlus results based on nucleotide sequences HOT 2
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