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)

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)

__weakref__

list of weak references to the object (if defined)

get_profile(gene, model_location)

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)

Handle a HMM protein profile

__init__(gene, cfg, path)

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__()

Returns:

the length of the HMM protein profile

Return type:

int

__str__()

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()

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)

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