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)[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)[source]¶

Initialize self. See help(type(self)) for accurate signature.

__weakref__¶

list of weak references to the object (if defined)

get_profile(gene, model_location)[source]¶

Parameters:

gene (macsypy.gene.Gene or macsypy.gene.Homolog or macsypy.gene.Analog object) – the gene associated to this profile

model_location (macsypy.registries.ModelLocation object.) – 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.

Return type:
macsypy.profile.Profile object

Profile¶

class macsypy.profile.Profile(gene, cfg, path)[source]¶

Handle a HMM protein profile

__init__(gene, cfg, path)[source]¶

Parameters:	gene (`macsypy.secretion.Gene` object) – the gene corresponding to this profile cfg (`macsypy.config.Config` object) – the configuration path (string) – the path to the hmm profile.

__len__()[source]¶

Returns:	the length of the HMM protein profile
Return type:	int

__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()[source]¶

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

Returns:	the length, presence of ga bit threshold
Return type:	tuple(int length, bool ga_threshold)

execute(cpu=1)[source]¶

Launch the Hmmer search (hmmsearch executable) with this profile

Parameters:	cpu (int) – the number of cpu to use for hmmsearch (must be >= 1)
Returns:	an object storing information on the results of the HMM search (HMMReport)
Return type:	`macsypy.report.HMMReport` object