ReferenceDB[BuscoDB]

Artifact containing BUSCO database for one or more lineages.

Artifact Format

class BuscoDatabaseDirFmt(model.DirectoryFormat):
    # File collections for text files
    (
        ancestral,
        dataset,
        lengths_cutoff,
        scores_cutoff,
        links_to_ODB,
        ancestral_variants,
        ogs_id,
        species,
        hmms,
        refseq_db_md5
    ) = [
            model.FileCollection(
                rf"busco_downloads\/lineages\/.+\/{pattern}",
                format=BuscoGenericTextFileFmt
            )
            for pattern in [
                r'ancestral$',
                r'dataset\.cfg$',
                r'lengths_cutoff$',
                r'scores_cutoff$',
                r'links_to_ODB.+\.txt$',
                r'ancestral_variants$',
                r'info\/ogs\.id\.info$',
                r'info\/species\.info$',
                r'hmms\/.+\.hmm$',
                r'refseq_db\.faa\.gz\.md5'
            ]
        ]

    # Placement_files. Optional because they are not in virus DB
    (
        list_of_reference_markers,
        mapping_taxid_lineage,
        mapping_taxids_busco_dataset_name,
        tree,
        tree_metadata,
    ) = [
            model.FileCollection(
                rf"busco_downloads\/placement_files\/{pattern}",
                format=BuscoGenericTextFileFmt,
                optional=True
            )
            for pattern in [
                r'list_of_reference_markers\..+\.txt$',
                r'mapping_taxid-lineage\..+\.txt$',
                r'mapping_taxids-busco_dataset_name\..+\.txt$',
                r'tree\..+\.nwk$',
                r'tree_metadata\..+\.txt$',
            ]
        ]

    # Others
    supermatrix_aln = model.FileCollection(
        r'busco_downloads\/placement_files\/supermatrix\.aln\..+\.faa$',
        format=AlignedProteinFASTAFormat,
        optional=True
    )
    prfls = model.FileCollection(
        r'busco_downloads\/lineages\/.+\/prfl\/.+\.prfl$',
        format=BuscoGenericTextFileFmt,
        optional=True
    )
    version_file = model.File(
        'busco_downloads/file_versions.tsv', format=BuscoGenericTextFileFmt
    )
    refseq_db = model.FileCollection(
        r'busco_downloads\/lineages\/.+refseq_db\.faa\.gz',
        format=BuscoGenericBinaryFileFmt
    )

Expected Folder Structure

data
└── busco_downloads
    ├── lineages
    │   ├── lineage_1
    │   │   ├── hmms
    │   │   ├── lengths_cutoff
    │   │   ├── ancestral
    │   │   ├── ancestral_variants
    │   │   ├── dataset.cfg
    │   │   ├── links_to_<dataset_version>.txt
    │   │   ├── refseq_db.faa.gz
    │   │   ├── refseq_db.faa.gz.md5
    │   │   ├── scores_cutoff
    │   │   └── info
    │   ⋮
    │   └── lineage_i
    │       ⋮
    └── placement_files

Where to find ReferenceDB[BUSCO]

• See MAG Quality Control tutorial for a full example.
• Actions in q2-moshpit that have this semantic type:

As Input

• qiime moshpit fetch-busco-db

As Output

• qiime moshpit evaluate-busco