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Data Models

nplinker.genomics

BGC 

BGC(id: str, /, *product_prediction: str)

Class to model BGC (biosynthetic gene cluster) data.

BGC data include both annotations and sequence data. This class is mainly designed to model the annotations or metadata.

The raw BGC data is stored in GenBank format (.gbk). Additional GenBank features could be added to the GenBank file to annotate BGCs, e.g. antiSMASH has some self-defined features (like region) in its output GenBank files.

The annotations of BGC can be stored in JSON format, which is defined and used by MIBiG.

Attributes:

  • id –

    BGC identifier, e.g. MIBiG accession, GenBank accession.

  • product_prediction –

    A tuple of (predicted) natural products or product classes of the BGC. For antiSMASH's GenBank data, the feature region /product gives product information. For MIBiG metadata, its biosynthetic class provides such info.

  • mibig_bgc_class (tuple[str] | None) –

    A tuple of MIBiG biosynthetic classes to which the BGC belongs. Defaults to None, which means the class is unknown.

    MIBiG defines 6 major biosynthetic classes for natural products, including NRP, Polyketide, RiPP, Terpene, Saccharide and Alkaloid. Note that natural products created by the other biosynthetic mechanisms fall under the category Other. For more details see the paper.

  • description (str | None) –

    Brief description of the BGC. Defaults to None.

  • smiles (tuple[str] | None) –

    A tuple of SMILES formulas of the BGC's products. Defaults to None.

  • antismash_file (str | None) –

    The path to the antiSMASH GenBank file. Defaults to None.

  • antismash_id (str | None) –

    Identifier of the antiSMASH BGC, referring to the feature VERSION of GenBank file. Defaults to None.

  • antismash_region (int | None) –

    AntiSMASH BGC region number, referring to the feature region of GenBank file. Defaults to None.

  • parents (set[GCF]) –

    The set of GCFs that contain the BGC.

  • strain (Strain | None) –

    The strain of the BGC.

Parameters:

  • id (str) –

    BGC identifier, e.g. MIBiG accession, GenBank accession.

  • product_prediction (str, default: () ) –

    BGC's (predicted) natural products or product classes.

Examples:

>>> bgc = BGC("Unique_BGC_ID", "Polyketide", "NRP")
>>> bgc.id
'Unique_BGC_ID'
>>> bgc.product_prediction
('Polyketide', 'NRP')
>>> bgc.is_mibig()
False
Source code in src/nplinker/genomics/bgc.py 
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def __init__(self, id: str, /, *product_prediction: str):
    """Initialize the BGC object.

    Args:
        id: BGC identifier, e.g. MIBiG accession, GenBank accession.
        product_prediction: BGC's (predicted) natural products or product classes.

    Examples:
        >>> bgc = BGC("Unique_BGC_ID", "Polyketide", "NRP")
        >>> bgc.id
        'Unique_BGC_ID'
        >>> bgc.product_prediction
        ('Polyketide', 'NRP')
        >>> bgc.is_mibig()
        False
    """
    # BGC metadata
    self.id = id
    self.product_prediction = product_prediction

    self.mibig_bgc_class: tuple[str] | None = None
    self.description: str | None = None
    self.smiles: tuple[str] | None = None

    # antismash related attributes
    self.antismash_file: str | None = None
    self.antismash_id: str | None = None  # version in .gbk, id in SeqRecord
    self.antismash_region: int | None = None  # antismash region number

    # other attributes
    self.parents: set[GCF] = set()
    self._strain: Strain | None = None

id instance-attribute 

id = id

product_prediction instance-attribute 

product_prediction = product_prediction

mibig_bgc_class instance-attribute 

mibig_bgc_class: tuple[str] | None = None

description instance-attribute 

description: str | None = None

smiles instance-attribute 

smiles: tuple[str] | None = None

antismash_file instance-attribute 

antismash_file: str | None = None

antismash_id instance-attribute 

antismash_id: str | None = None

antismash_region instance-attribute 

antismash_region: int | None = None

parents instance-attribute 

parents: set[GCF] = set()

strain property writable 

strain: Strain | None

Get the strain of the BGC.

bigscape_classes property 

bigscape_classes: set[str | None]

Get BiG-SCAPE's BGC classes.

BiG-SCAPE's BGC classes are similar to those defined in MiBIG but have more categories (7 classes), including:

  • NRPS
  • PKS-NRP_Hybrids
  • PKSI
  • PKSother
  • RiPPs
  • Saccharides
  • Terpene

For BGC falls outside of these categories, the value is "Others".

Default is None, which means the class is unknown.

More details see: https://doi.org/10.1038%2Fs41589-019-0400-9.

aa_predictions property 

aa_predictions: list

Amino acids as predicted monomers of product.

Returns:

  • list –

    list of dicts with key as amino acid and value as prediction

  • list –

    probability.

__repr__ 

__repr__()
Source code in src/nplinker/genomics/bgc.py 
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def __repr__(self):
    return str(self)

__str__ 

__str__()
Source code in src/nplinker/genomics/bgc.py 
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def __str__(self):
    return "{}(id={}, strain={}, asid={}, region={})".format(
        self.__class__.__name__,
        self.id,
        self.strain,
        self.antismash_id,
        self.antismash_region,
    )

__eq__ 

__eq__(other) -> bool
Source code in src/nplinker/genomics/bgc.py 
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def __eq__(self, other) -> bool:
    if isinstance(other, BGC):
        return self.id == other.id and self.product_prediction == other.product_prediction
    return NotImplemented

__hash__ 

__hash__() -> int
Source code in src/nplinker/genomics/bgc.py 
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def __hash__(self) -> int:
    return hash((self.id, self.product_prediction))

__reduce__ 

__reduce__() -> tuple

Reduce function for pickling.

Source code in src/nplinker/genomics/bgc.py 
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def __reduce__(self) -> tuple:
    """Reduce function for pickling."""
    return (self.__class__, (self.id, *self.product_prediction), self.__dict__)

add_parent 

add_parent(gcf: GCF) -> None

Add a parent GCF to the BGC.

Parameters:

  • gcf (GCF) –

    gene cluster family

Source code in src/nplinker/genomics/bgc.py 
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def add_parent(self, gcf: GCF) -> None:
    """Add a parent GCF to the BGC.

    Args:
        gcf: gene cluster family
    """
    gcf.add_bgc(self)

detach_parent 

detach_parent(gcf: GCF) -> None

Remove a parent GCF.

Source code in src/nplinker/genomics/bgc.py 
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def detach_parent(self, gcf: GCF) -> None:
    """Remove a parent GCF."""
    gcf.detach_bgc(self)

is_mibig 

is_mibig() -> bool

Check if the BGC is a MIBiG reference BGC or not.

Warning

This method evaluates MIBiG BGC based on the pattern that MIBiG BGC names start with "BGC". It might give false positive result.

Returns:

  • bool –

    True if it's MIBiG reference BGC

Source code in src/nplinker/genomics/bgc.py 
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def is_mibig(self) -> bool:
    """Check if the BGC is a MIBiG reference BGC or not.

    Warning:
        This method evaluates MIBiG BGC based on the pattern that MIBiG
        BGC names start with "BGC". It might give false positive result.

    Returns:
        True if it's MIBiG reference BGC
    """
    return self.id.startswith("BGC")

GCF 

GCF(id: str)

Class to model gene cluster family (GCF).

GCF is a group of similar BGCs and generated by clustering BGCs with tools such as BiG-SCAPE and BiG-SLICE.

Attributes:

  • id –

    id of the GCF object.

  • bgc_ids (set[str]) –

    a set of BGC ids that belongs to the GCF.

  • bigscape_class (str | None) –

    BiG-SCAPE's BGC class. BiG-SCAPE's BGC classes are similar to those defined in MiBIG but have more categories (7 classes), including:

    • NRPS
    • PKS-NRP_Hybrids
    • PKSI
    • PKSother
    • RiPPs
    • Saccharides
    • Terpene

    For BGC falls outside of these categories, the value is "Others".

    Default is None, which means the class is unknown.

    More details see: https://doi.org/10.1038%2Fs41589-019-0400-9.

Parameters:

  • id (str) –

    id of the GCF object.

Examples:

>>> gcf = GCF("Unique_GCF_ID")
>>> gcf.id
'Unique_GCF_ID'
Source code in src/nplinker/genomics/gcf.py 
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def __init__(self, id: str, /) -> None:
    """Initialize the GCF object.

    Args:
        id: id of the GCF object.

    Examples:
        >>> gcf = GCF("Unique_GCF_ID")
        >>> gcf.id
        'Unique_GCF_ID'
    """
    self.id = id
    self.bgc_ids: set[str] = set()
    self.bigscape_class: str | None = None
    self._bgcs: set[BGC] = set()
    self._strains: StrainCollection = StrainCollection()

id instance-attribute 

id = id

bgc_ids instance-attribute 

bgc_ids: set[str] = set()

bigscape_class instance-attribute 

bigscape_class: str | None = None

bgcs property 

bgcs: set[BGC]

Get the BGC objects.

strains property 

strains: StrainCollection

Get the strains in the GCF.

__str__ 

__str__() -> str
Source code in src/nplinker/genomics/gcf.py 
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def __str__(self) -> str:
    return (
        f"GCF(id={self.id}, #BGC_objects={len(self.bgcs)}, #bgc_ids={len(self.bgc_ids)},"
        f"#strains={len(self._strains)})."
    )

__repr__ 

__repr__() -> str
Source code in src/nplinker/genomics/gcf.py 
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def __repr__(self) -> str:
    return str(self)

__eq__ 

__eq__(other) -> bool
Source code in src/nplinker/genomics/gcf.py 
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def __eq__(self, other) -> bool:
    if isinstance(other, GCF):
        return self.id == other.id and self.bgcs == other.bgcs
    return NotImplemented

__hash__ 

__hash__() -> int

Hash function for GCF.

Note that GCF class is a mutable container. We only hash the GCF id to avoid the hash value changes when self._bgcs is updated.

Source code in src/nplinker/genomics/gcf.py 
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def __hash__(self) -> int:
    """Hash function for GCF.

    Note that GCF class is a mutable container. We only hash the GCF id to
    avoid the hash value changes when `self._bgcs` is updated.
    """
    return hash(self.id)

__reduce__ 

__reduce__() -> tuple

Reduce function for pickling.

Source code in src/nplinker/genomics/gcf.py 
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def __reduce__(self) -> tuple:
    """Reduce function for pickling."""
    return (self.__class__, (self.id,), self.__dict__)

add_bgc 

add_bgc(bgc: BGC) -> None

Add a BGC object to the GCF.

Source code in src/nplinker/genomics/gcf.py 
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def add_bgc(self, bgc: BGC) -> None:
    """Add a BGC object to the GCF."""
    bgc.parents.add(self)
    self._bgcs.add(bgc)
    self.bgc_ids.add(bgc.id)
    if bgc.strain is not None:
        self._strains.add(bgc.strain)
    else:
        logger.warning("No strain specified for the BGC %s", bgc.id)

detach_bgc 

detach_bgc(bgc: BGC) -> None

Remove a child BGC object.

Source code in src/nplinker/genomics/gcf.py 
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def detach_bgc(self, bgc: BGC) -> None:
    """Remove a child BGC object."""
    bgc.parents.remove(self)
    self._bgcs.remove(bgc)
    self.bgc_ids.remove(bgc.id)
    if bgc.strain is not None:
        for other_bgc in self._bgcs:
            if other_bgc.strain == bgc.strain:
                return
        self._strains.remove(bgc.strain)

has_strain 

has_strain(strain: Strain) -> bool

Check if the given strain exists.

Parameters:

  • strain (Strain) –

    Strain object.

Returns:

  • bool –

    True when the given strain exist.

Source code in src/nplinker/genomics/gcf.py 
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def has_strain(self, strain: Strain) -> bool:
    """Check if the given strain exists.

    Args:
        strain: `Strain` object.

    Returns:
        True when the given strain exist.
    """
    return strain in self._strains

has_mibig_only 

has_mibig_only() -> bool

Check if the GCF's children are only MIBiG BGCs.

Returns:

  • bool –

    True if GCF.bgc_ids are only MIBiG BGC ids.

Source code in src/nplinker/genomics/gcf.py 
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def has_mibig_only(self) -> bool:
    """Check if the GCF's children are only MIBiG BGCs.

    Returns:
        True if `GCF.bgc_ids` are only MIBiG BGC ids.
    """
    return all(map(lambda id: id.startswith("BGC"), self.bgc_ids))

is_singleton 

is_singleton() -> bool

Check if the GCF contains only one BGC.

Returns:

  • bool –

    True if GCF.bgc_ids contains only one BGC id.

Source code in src/nplinker/genomics/gcf.py 
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def is_singleton(self) -> bool:
    """Check if the GCF contains only one BGC.

    Returns:
        True if `GCF.bgc_ids` contains only one BGC id.
    """
    return len(self.bgc_ids) == 1