GC-AssemblyDesc

Defined in file genome_collection.asn
C++ class: CGC_AssemblyDesc


GC-AssemblyDesc ::= SEQUENCE {
    -- project ID for this genome
    -- this is the ID for this asssembly and may reflect the submitter/source
    projects SET OF GC-Project OPTIONAL,

    -- Names of the assembly
    name VisibleString OPTIONAL,
    submitter-name VisibleString OPTIONAL,
    display-name VisibleString OPTIONAL,
    long-name UTF8String OPTIONAL,
    filesafe-name VisibleString OPTIONAL,
    wgs-acc-prefix VisibleString OPTIONAL,
    wgs-acc-number INTEGER OPTIONAL,

    -- release type: RefSeq / GenBank.
    release-type INTEGER {
        genbank (1),
        refseq(2)
    } OPTIONAL,

    -- release status (numeric values have gaps for possible additional states
    release-status INTEGER {
        new(0),
        gpipe(5),
        public(10),
        suppressed(15),
        hup(100),
        withdrawn(105)
    } OPTIONAL,

    -- in alt-loci units - contain alignment of this sequence to the primary
    -- unit
    annot SET OF Seq-annot OPTIONAL,

    -- Synonyms: Other releases of same assembly
    synonyms   SET OF GC-DbTagAlias OPTIONAL,

    -- Submitter release date
    submitter-date Date OPTIONAL,

    -- Various attributes assigned at this level:
    -- biosrc, comments, publications...
    --
    -- Special user-objects:
    -- Internal identifiers (GCOL-1178):  type  str ="gencoll-misc"
    --              data : 2 user fields :
    --              label  str "asm-name" str 
    --              label  str "asm-id" int 
    -- ftp-sites:  type  str ="ftp-sites"
    --              data : one or 2 fields, depending if both GB and RS have ftp-sites
    --              label  str : "genbank" or "refseq" str : path to ftp-site
    -- diffs between GB / RS assemblies: type str "diff-from-synonym",
    --         data label id  str 

    descr Seq-descr OPTIONAL ,

    -- flag: is this assembly partial?
    -- **NOTE: not set = not known!!
    partial BOOLEAN OPTIONAL,

    -- level of coverage for this assembly
    -- **NOTE: not set = not known!!
    coverage REAL OPTIONAL,

    -- release level: Most of releases are major
    release-level INTEGER {
        major(0),
        patch(1),
        minor(2),
        -- stopper
        other(255)
    } DEFAULT major,

    -- organization which submitted this assembly.
    -- populated from BioProject
    submitter-organization UTF8String OPTIONAL
}