profile

The Profile object is used for the search of the gene with Hmmer. A “Profile” must match a HMM protein profile file, which name is based on the profile name. For instance, the gspG gene has the corresponding “gspG.hmm” profile file provided at a dedicated location.

profile API reference

ProfileFactory

class macsypy.profile.ProfileFactory(cfg: Config | NoneConfig)[source]

Build and store all Profile objects. Profiles must not be instanciated directly. The profile_factory must be used. The profile_factory ensures there is only one instance of profile for a given name. To get a profile, use the method get_profile. If the profile is already cached, this instance is returned. Otherwise, a new profile is built, stored in the profile_factory and then returned.

__init__(cfg: Config | NoneConfig) → None[source]
__weakref__

list of weak references to the object (if defined)

get_profile(gene: CoreGene, model_location: ModelLocation) → Profile[source]
Parameters:

  • gene – the gene associated to this profile

  • model_location – The where to get the profile

Returns:

The profile corresponding to the name. If the profile already exists, return it. Otherwise, build it, store it and return it.

Profile

class macsypy.profile.Profile(gene: CoreGene, cfg: Config, path: str)[source]

Handle a HMM protein profile

__init__(gene: CoreGene, cfg: Config, path: str) → None[source]
Parameters:

  • gene – the gene corresponding to this profile

  • cfg – the configuration

  • path – the path to the hmm profile.

__len__() → int[source]
Returns:

the length of the HMM protein profile

Return type:

int

__str__() → str[source]

Print the name of the corresponding gene and the path to the HMM profile.

__weakref__

list of weak references to the object (if defined)

_profile_features() → tuple[int, bool][source]

Parse the HMM profile to extract the length and the presence of GA bit threshold

Returns:

the length, presence of ga bit threshold

execute(cpu: int = 1) → HMMReport | None[source]

Launch the Hmmer search (hmmsearch executable) with this profile

Parameters:

cpu – the number of cpu to use for hmmsearch (must be >= 1)

Returns:

an object storing information on the results of the HMM search (HMMReport)