mecfs_bio.assets.reference_data.genome_sequence.ucsc_hg19_fasta

UCSC hg19 (GRCh37) genome sequence, pinned by the md5 UCSC publishes in md5sum.txt.

The indexed form is what genome-reference harmonization reads. It is wrapped in DiscardDepsWrapper, so only the uncompressed FASTA and its .fai are stored, not the gzipped download as well. Note that UCSC hg19 chrM is not the rCRS mitochondrial sequence, which is why harmonization excludes MT by default.

Attributes:

• UCSC_HG19_FASTA_GZ –
• UCSC_HG19_INDEXED_FASTA –

UCSC_HG19_FASTA_GZ module-attribute

UCSC_HG19_FASTA_GZ = DownloadFileTask(
    meta=ReferenceFileMeta(
        id="ucsc_hg19_fasta_gz",
        group="genome_sequence",
        sub_group="ucsc_hg19",
        sub_folder=PurePath("raw"),
        extension=".fa.gz",
    ),
    url="https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.fa.gz",
    md5_hash="806c02398f5ac5da8ffd6da2d1d5d1a9",
)

UCSC_HG19_INDEXED_FASTA module-attribute

UCSC_HG19_INDEXED_FASTA = DiscardDepsWrapper(
    IndexedFastaTask.create(
        fasta_gz_task=UCSC_HG19_FASTA_GZ,
        asset_id="ucsc_hg19_indexed_fasta",
        build="19",
    )
)