Comments (4)
👍 for updating the places where qiime2 is reading/writing manifests so they're compatible with commas. There'll still be the opportunity for users to run into the issue when they're writing their own manifest file (which they'll need to quote themselves), so some docs on the importing tutorial may be useful in addition to the q2-types updates. Does that sound good to you?
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Sounds good to me (updating q2-types and documenting the edge case)!
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I'm not sure we can do much about that since the format is CSV. Users will need to quote any fields containing commas to "escape" the delimiter. Do you think describing this edge-case in the "fastq manifest" part of the importing tutorial would resolve the issue?
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Couldn't we start emitting quoted fields and/or escaped fields in the internal manifest? It looks like we are already using pandas.read_csv
, to read those manifests back into Q2, which should be able to handle quoted vs non-quoted editions of these files. I think we could do that in a backwards-compatible way, but maybe I am missing something! One gotcha is that there are a few places in the ecosystem where we grab the manifest and do some things with it, so depending on how that is currently implemented, there could be some unintended consequences 👿 .
I am up for documenting the edge case if we don't have a quick fix for this!
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Related Issues (20)
- new format / transformer for single-end demuliplexed files named by sample id HOT 1
- add usage examples to artifact classes HOT 1
- deprecation warning on import of type `SampleData[PairedEndSequencesWithQuality]` with format `PairedEndFastqManifestPhred33V2`
- add `ImmutableMetadata` semantic type
- FEAT: Importing multiplexed paired-end data with separated barcode sequence files HOT 1
- Migrate FeatureMap from q2-types-genomics to q2-types
- Blast6 file empty HOT 1
- MAINT: Migrate q2-types-genomics types/formats/transformers into q2-types
- Patch to work with Pandas 2.x HOT 1
- FEAT: Importing sequence data from BIOM files HOT 5
- ENH: Semantic type for HMMER database
- MAINT: Implement a validation method for the `OrthologFileFmt` HOT 2
- ENH: Add new type `FeatureData[SequenceCharacteristics]`
- ENH: add `ReferenceDB[HMMER]` semantic type
- IMP: PacBio Phred Offset is Incorrectly Translated HOT 1
- add manifest formats to q2-types, and update throughout the shotgun distro to use those
- MAINT: Move partitioning and collating actions from q2-moshpit to q2-types
- iteritems deprecation warning on merge_seqs HOT 1
- identifiers are being parsed as feature labels in various visualizations HOT 1
- ENH: Adding new type called `FeatureTable[Normalized]`
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