Struct NcbiContigEntry 

pub struct NcbiContigEntry {
    pub sequence_name: String,
    pub length: u64,
    pub genbank_accn: Option<String>,
    pub refseq_accn: Option<String>,
    pub ucsc_name: Option<String>,
    pub role: Option<String>,
    pub assigned_molecule: Option<String>,
    pub patch_type: Option<PatchType>,
}

A parsed contig from an NCBI assembly report with all naming variants

Fields

sequence_name: String

Primary sequence name (from Sequence-Name column)

length: u64

Sequence length

genbank_accn: Option<String>

GenBank accession

refseq_accn: Option<String>

RefSeq accession

ucsc_name: Option<String>

UCSC-style name

role: Option<String>

Sequence role (e.g., “assembled-molecule”, “unlocalized-scaffold”)

assigned_molecule: Option<String>

Assigned molecule (chromosome number, e.g., “1”, “X”, “Y”, “MT”)

patch_type: Option<PatchType>

Patch type if this is a patch contig

Implementations

impl NcbiContigEntry

pub fn all_names_with_options(&self, generate_ucsc_names: bool) -> Vec<String>

Get all unique, non-empty names for this contig as aliases.

Arguments

• generate_ucsc_names - If true and this is a patch contig without a UCSC-style name in the assembly report, generate one using the UCSC naming convention. This is useful for assembly reports prior to p13 where patch UCSC names were not included.

UCSC Name Generation

When generate_ucsc_names is true and:

• This contig is a fix-patch or novel-patch (determined from sequence role)
• The UCSC-style-name column is “na” or missing
• The GenBank accession and assigned molecule are available

Then a UCSC-style name will be generated following the convention: chr{chromosome}_{accession}v{version}_{suffix}

Where suffix is _fix for fix-patches and _alt for novel-patches.

Sources

• UCSC FAQ: https://genome.ucsc.edu/FAQ/FAQdownloads.html
• UCSC Patches blog: https://genome-blog.soe.ucsc.edu/blog/2019/02/22/patches/
• Verified against: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/p12/

pub fn to_contig(&self) -> Contig

Convert to a Contig with aliases populated.

This is equivalent to calling to_contig_with_options(true) - UCSC name generation is enabled by default.

pub fn to_contig_with_options(&self, generate_ucsc_names: bool) -> Contig

Convert to a Contig with aliases populated.

Arguments

• generate_ucsc_names - If true, generate UCSC-style names for patches that don’t have them in the assembly report. See Self::all_names_with_options for details on the naming convention.

Trait Implementations

impl Clone for NcbiContigEntry

fn clone(&self) -> NcbiContigEntry

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for NcbiContigEntry

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.