Enum ModType 

pub enum ModType {
    SixMA,
    FiveMC,
    FourMC,
}

Represents a DNA base modification type.

This enum defines the types of modifications that can occur on DNA bases, including their associated codes for parsing and visualization.

Variants

• SixMA: N6-methyladenine (6mA), represented by the pileup code a.
• FiveMC: 5-methylcytosine (5mC), represented by the pileup code m.
• FourMC: 4-methylcytosine (4mC), represented by the pileup code 21839.

Examples

use epimetheus_methylome::ModType;

let mod_type = ModType::SixMA;
assert_eq!(mod_type.to_pileup_code(), "a");

Variants

SixMA

FiveMC

FourMC

Implementations

impl ModType

pub fn to_pileup_code(&self) -> &'static str

Returns the pileup code corresponding to the modification type.

Pileup codes are compact representations of modification types used in sequencing data (or maybe just modkit):

• SixMA (6mA): "a"
• FiveMC (5mC): "m"
• FourMC (4mC): "21839"

Examples

use epimetheus_methylome::ModType;

let mod_type = ModType::FiveMC;
assert_eq!(mod_type.to_pileup_code(), "m");

pub fn from_sam_code(base: char, modification: &str) -> Option<Self>

Passes the sam header tag to ModType

Sam tags have the following and more for the methylation types: MM:Z:{*}

• A+a (6mA): "a"
• C+m (5mC): "m"
• C+21839 (4mC): "21839"

Examples

use epimetheus_methylome::ModType;

assert_eq!(ModType::from_sam_code('A', "a"), Some(ModType::SixMA));

Trait Implementations

impl Clone for ModType

fn clone(&self) -> ModType

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for ModType

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

Formats the value using the given formatter.

impl Display for ModType

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

Formats the modification type for display purposes.

Each modification type is represented in the format: <Modification Name> (<Pileup Code>).

For example:

• 6mA (a) for SixMA
• 5mC (m) for FiveMC
• 4mC (21839) for FourMC

Examples

use epimetheus_methylome::ModType;

let mod_type = ModType::FourMC;
assert_eq!(format!("{}", mod_type), "4mC (21839)");

impl FromStr for ModType

Parses a modification type from a string.

The input string must match one of the following:

• "a" for SixMA (6mA)
• "m" for FiveMC (5mC)
• "21839" for FourMC (4mC)

Arguments

• mod_type: A string slice representing the modification type.

Returns

• Ok(ModType) if the string matches a supported modification type.
• Err if the string does not match any supported modification type.

Examples

use epimetheus_methylome::ModType;

let mod_type = "a".parse::<ModType>().unwrap();
assert_eq!(mod_type, ModType::SixMA);

let invalid = "unsupported".parse::<ModType>();
assert!(invalid.is_err());

type Err = Error

The associated error which can be returned from parsing.

fn from_str(s: &str) -> Result<Self, Self::Err>

Parses a string s to return a value of this type.

impl Hash for ModType

fn hash<__H: Hasher>(&self, state: &mut __H)

Feeds this value into the given Hasher.

fn hash_slice<H>(data: &[Self], state: &mut H)

where H: Hasher, Self: Sized,

Feeds a slice of this type into the given Hasher.

impl Ord for ModType

fn cmp(&self, other: &ModType) -> Ordering

This method returns an Ordering between self and other.

fn max(self, other: Self) -> Self

where Self: Sized,

Compares and returns the maximum of two values.

fn min(self, other: Self) -> Self

where Self: Sized,

Compares and returns the minimum of two values.

fn clamp(self, min: Self, max: Self) -> Self

where Self: Sized,

Restrict a value to a certain interval.

impl PartialEq for ModType

fn eq(&self, other: &ModType) -> bool

Tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

Tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl PartialOrd for ModType

fn partial_cmp(&self, other: &ModType) -> Option<Ordering>

This method returns an ordering between self and other values if one exists.

fn lt(&self, other: &Rhs) -> bool

Tests less than (for self and other) and is used by the < operator.

fn le(&self, other: &Rhs) -> bool

Tests less than or equal to (for self and other) and is used by the <= operator.

fn gt(&self, other: &Rhs) -> bool

Tests greater than (for self and other) and is used by the > operator.

fn ge(&self, other: &Rhs) -> bool

Tests greater than or equal to (for self and other) and is used by the >= operator.

impl Copy for ModType

impl Eq for ModType

impl StructuralPartialEq for ModType