Profile API

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.

ProfileFactory API reference

class macsypy.gene.ProfileFactory

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.

get_profile(gene, cfg, profiles_registry)

Parameters:

• gene (macsypy.gene.Gene or macsypy.gene.Homolog or macsypy.gene.Analog object) – the gene associated to this profile
• profiles_registry (the registry of profiles) – the registry where are stored the path of the profiles
• profiles_registry – macsypy.registries.ProfilesRegistry instance.

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.gene.Profile object

Profile API reference

class macsypy.gene.Profile(gene, cfg, path)

Handle a HMM protein profile

__init__(gene, cfg, path)

Parameters:

• gene – 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)

_len()

Parse the HMM profile file to get and store the length. This private method is called at the Profile init.

execute()

Launch the Hmmer search (hmmsearch executable) with this profile

Returns:an object storing information on th results of the HMM search (HMMReport) Return type:macsypy.report.HMMReport object