qiime2 / q2-types

qiime2/q2-types Issues

IMP: PacBio Phred Offset is Incorrectly Translated
Updated 2 months ago
Patch to work with Pandas 2.x
Closed 2 months ago1
ENH: Add new type `FeatureData[SequenceCharacteristics]`
Closed 2 months ago
ENH: add `ReferenceDB[HMMER]` semantic type
Updated 2 months ago
ENH: Semantic type for HMMER database
Closed 2 months ago
MAINT: Implement a validation method for the `OrthologFileFmt`
Updated 3 months ago
FEAT: Importing sequence data from BIOM files
Updated 4 months ago5
MAINT: Migrate q2-types-genomics types/formats/transformers into q2-types
Closed 5 months ago
zipped fasta gets imported and fails silently
Closed 9 months ago1
FEAT: Importing multiplexed paired-end data with separated barcode sequence files
Updated 9 months ago1
Blast6 file empty
Closed 10 months ago1
Migrate FeatureMap from q2-types-genomics to q2-types
Closed 10 months ago
EMP formats require Phred designation
Closed 10 months ago2
add usage examples to artifact classes
Updated a year ago1
add `ImmutableMetadata` semantic type
Closed a year ago
deprecation warning on import of type `SampleData[PairedEndSequencesWithQuality]` with format `PairedEndFastqManifestPhred33V2`
Closed a year ago
new format / transformer for single-end demuliplexed files named by sample id
Closed 2 years ago1
add types, formats, and transformers for legacy 454 data
Closed 2 years ago1
Transform SLPSSEFDF -> CasavaOneEightSingleLanePerSampleDirFmt
Closed 4 years ago2
Conflict with biom-format 2.1.12
Updated 2 years ago
ENH: transformer for BLAST6Format --> Metadata
Closed 2 years ago
ENH: new type + format for BLASTDB v5
Updated 2 years ago
Transformer from Newick to dendropy
Updated 2 years ago1
Change Newick validation from `sniff` to `validate`
Updated 4 years ago1
Support FASTA files which contain all reads per sample (i.e. not just representative seqs)
Updated 4 years ago
Feature table IDs not guaranteed to work with Metadata IDs
Updated 4 years ago
Support transforming `QIIME1DemuxDirFmt` to `SingleLanePerSampleSingleEndFastqDirFmt`
Updated 4 years ago1
Support OrdinationFormat -> pd.Dataframe transformation
Updated 4 years ago
BUG: users can create incomplete SingleLanePerSamplePairedEndFastqDirFmt
Closed 4 years ago5
Move matplotlib pin to >=3.2
Closed 4 years ago2
Laneless Casava transformers are broken
Closed 4 years ago1
TSVTaxonomyFormat should check for empty column labels
Closed 5 years ago4
Validate paired-end sets are record-matched
Updated 5 years ago1
qiime 'taxonomy' tabulate error
Closed 5 years ago2
DEP: pandas 0.25.x updates
Closed 5 years ago
Importing manifest v1 without sample names produce unclear error
Updated 5 years ago1
PHRED64 variants of Multiplexed*EndBarcodeInSequence
Updated 5 years ago1
Handle whitespace in TSVTaxonomyFormat -> Metadata transformer
Closed 5 years ago7
FeatureData[Taxonomy] validator: check for whitespace in accession #s
Closed 5 years ago1
Differential type
Closed 5 years ago1
DNAFASTAFormat validator is not catching invalid DNA characters
Closed 5 years ago11
Revert scipy to an older version to correct statsmodels conflict.
Closed 5 years ago
Metadata-compatible Manifest formats
Closed 5 years ago2
Validate that per-sample-seqs sets aren't empty
Updated 5 years ago
CRLF line endings + fasta (or other text file formats?) = big headache
Updated 5 years ago
ENH: transformer: FeatureTable[*] -> Metadata
Closed 6 years ago
BUG: SampleData[AlphaDiversity] -> Metadata doesn't work with tuples
Updated 6 years ago1
DNAFASTAFormat and AlignedDNAFASTAFormat should check for duplicate ids during full validation
Updated 6 years ago
Strip whitespace from fields in manifest formats
Closed 6 years ago
Allow additional columns in `AlphaDiversityFormat`
Closed 6 years ago