mecfs_bio.assets.reference_data.genome_sequence.ucsc_hg38_fasta

UCSC hg38 (GRCh38) genome sequence, pinned by the md5 UCSC publishes in md5sum.txt.

Used to tune the stringent ambiguous-indel rules on build-38 DecodeME, whose source orientation is fully reference-consistent. Wrapped in DiscardDepsWrapper so only the uncompressed FASTA and its .fai are stored.

Attributes:

• UCSC_HG38_FASTA_GZ –
• UCSC_HG38_INDEXED_FASTA –

UCSC_HG38_FASTA_GZ module-attribute

UCSC_HG38_FASTA_GZ = DownloadFileTask(
    meta=ReferenceFileMeta(
        id="ucsc_hg38_fasta_gz",
        group="genome_sequence",
        sub_group="ucsc_hg38",
        sub_folder=PurePath("raw"),
        extension=".fa.gz",
    ),
    url="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz",
    md5_hash="1c9dcaddfa41027f17cd8f7a82c7293b",
)

UCSC_HG38_INDEXED_FASTA module-attribute

UCSC_HG38_INDEXED_FASTA = DiscardDepsWrapper(
    IndexedFastaTask.create(
        fasta_gz_task=UCSC_HG38_FASTA_GZ,
        asset_id="ucsc_hg38_indexed_fasta",
        build="38",
    )
)